Mercurial > repos > galaxytrakr > hfp_centriflaken_awsbatch
changeset 0:082e0091e813 draft default tip
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/LICENSE.md Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,98 @@ +# CPIPES (CFSAN PIPELINES) + +## The modular pipeline repository at CFSAN, FDA + +**CPIPES** (CFSAN PIPELINES) is a collection of modular pipelines based on **NEXTFLOW**, +mostly for bioinformatics data analysis at **CFSAN, FDA.** + +--- + +### **LICENSES** + +\ + + +**CPIPES** is licensed under: + +```text +MIT License + +In the U.S.A. Public Domain; elsewhere Copyright (c) 2022 U.S. Food and Drug Administration + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. +``` + +\ + + +Portions of **CPIPES** are built on modified versions of many tools, scripts and libraries from [nf-core/modules](https://github.com/nf-core/modules) and [nf-core/rnaseq](https://github.com/nf-core/rna-seq) which are originally licensed under: + +```text +MIT License + +Copyright (c) Philip Ewels +Copyright (c) Phil Ewels, Rickard Hammarén + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. +``` + +\ + + +The **MultiQC** report, in addition uses [DataTables](https://datatables.net), which is licensed under: + +```text +MIT License + +Copyright (C) 2008-2022, SpryMedia Ltd. + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. +```
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/README.md Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,59 @@ +# `centriflaken` + +`centriflaken` is an automated precision metagenomics workflow for assembly and _in silico_ analyses of food-borne pathogens. `centriflaken` primarily fine-tuned for detecting and classifying Shiga toxin-producing **_Escherichia coli_** (**STEC**), can also be used for performing analyses on other food-borne pathogens such as **_Salmonella enterica_**. `centriflaken` takes as input a UNIX path to FASTQ, generates MAGs, and performs in silico-based analysis for STECs as described in [Maguire et al. 2021](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0245172). + +`centriflaken` works on both **Illumina** short reads and **Oxford Nanopore** long reads. + +It is written in **Nextflow** and is part of the modular data analysis pipelines at **HFP**. + +\ + + +## Workflows + +**CPIPES**: + +- `centriflaken` : [README](./readme/centriflaken.md). +- `centriflaken_hy` : [README](./readme/centriflaken.md#illumina-short-reads). + +\ + + +### Citing `centriflaken` + +--- +Manuscript in preparation. + +> +>**centriflaken: an automated data analysis pipeline for assembly and in silico analyses of food-borne pathogens from metagenomic samples.** +> +>Kranti Konganti, Julie Kase, and Narjol Gonzalez-Escalona. +> + +\ + + +### Future work + +--- + +- Incorporation of ANI methods to speed up the analysis methods. +- Incorporation of Oxford Nanopore models for barcode level assembly. + +\ + + +### Caveats + +--- + +- The main workflow has been used for **research purposes** only. +- Analysis results should be interpreted with caution. + +\ + + +### Disclaimer + +--- +**HFP, FDA** assumes no responsibility whatsoever for use by other parties of the Software, its source code, documentation or compiled or uncompiled executables, and makes no guarantees, expressed or implied, about its quality, reliability, or any other characteristic. Further, **HFP, FDA** makes no representations that the use of the Software will not infringe any patent or proprietary rights of third parties. The use of this code in no way implies endorsement by the **HFP, FDA** or confers any advantage in regulatory decisions.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/assets/dummy_file.txt Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,1 @@ +DuMmY
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/assets/dummy_file2.txt Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,1 @@ +DuMmY
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/bin/check_samplesheet.py Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,185 @@ +#!/usr/bin/env python3 + +import os +import sys +import errno +import argparse + + +def parse_args(args=None): + Description = "Reformat samplesheet file and check its contents." + Epilog = "Example usage: python check_samplesheet.py <FILE_IN> <FILE_OUT>" + + parser = argparse.ArgumentParser(description=Description, epilog=Epilog) + parser.add_argument("FILE_IN", help="Input samplesheet file.") + parser.add_argument("FILE_OUT", help="Output file.") + return parser.parse_args(args) + + +def make_dir(path): + if len(path) > 0: + try: + os.makedirs(path) + except OSError as exception: + if exception.errno != errno.EEXIST: + raise exception + + +def print_error(error, context="Line", context_str=""): + error_str = f"ERROR: Please check samplesheet -> {error}" + if context != "" and context_str != "": + error_str = f"ERROR: Please check samplesheet -> {error}\n{context.strip()}: '{context_str.strip()}'" + print(error_str) + sys.exit(1) + + +def check_samplesheet(file_in, file_out): + """ + This function checks that the samplesheet follows the following structure: + + sample,fq1,fq2,strandedness + SAMPLE_PE,SAMPLE_PE_RUN1_1.fastq.gz,SAMPLE_PE_RUN1_2.fastq.gz,forward + SAMPLE_PE,SAMPLE_PE_RUN2_1.fastq.gz,SAMPLE_PE_RUN2_2.fastq.gz,forward + SAMPLE_SE,SAMPLE_SE_RUN1_1.fastq,,forward + SAMPLE_SE,SAMPLE_SE_RUN1_2.fastq.gz,,forward + + For an example see: + https://github.com/nf-core/test-datasets/blob/rnaseq/samplesheet/v3.1/samplesheet_test.csv + """ + + sample_mapping_dict = {} + with open(file_in, "r", encoding='utf-8-sig') as fin: + + ## Check header + MIN_COLS = 3 + HEADER = ["sample", "fq1", "fq2", "strandedness"] + header = [x.strip('"') for x in fin.readline().strip().split(",")] + if header[: len(HEADER)] != HEADER: + print( + f"ERROR: Please check samplesheet header -> {','.join(header)} != {','.join(HEADER)}" + ) + sys.exit(1) + + ## Check sample entries + for line in fin: + if line.strip(): + lspl = [x.strip().strip('"') for x in line.strip().split(",")] + + ## Check valid number of columns per row + if len(lspl) < len(HEADER): + print_error( + f"Invalid number of columns (minimum = {len(HEADER)})!", + "Line", + line, + ) + + num_cols = len([x for x in lspl if x]) + if num_cols < MIN_COLS: + print_error( + f"Invalid number of populated columns (minimum = {MIN_COLS})!", + "Line", + line, + ) + + ## Check sample name entries + sample, fq1, fq2, strandedness = lspl[: len(HEADER)] + if sample.find(" ") != -1: + print( + f"WARNING: Spaces have been replaced by underscores for sample: {sample}" + ) + sample = sample.replace(" ", "_") + if not sample: + print_error("Sample entry has not been specified!", "Line", line) + + ## Check FastQ file extension + for fastq in [fq1, fq2]: + if fastq: + if fastq.find(" ") != -1: + print_error("FastQ file contains spaces!", "Line", line) + # if not fastq.endswith(".fastq.gz") and not fastq.endswith(".fq.gz"): + # print_error( + # "FastQ file does not have extension '.fastq.gz' or '.fq.gz'!", + # "Line", + # line, + # ) + + ## Check strandedness + strandednesses = ["unstranded", "forward", "reverse"] + if strandedness: + if strandedness not in strandednesses: + print_error( + f"Strandedness must be one of '{', '.join(strandednesses)}'!", + "Line", + line, + ) + else: + print_error( + f"Strandedness has not been specified! Must be one of {', '.join(strandednesses)}.", + "Line", + line, + ) + + ## Auto-detect paired-end/single-end + sample_info = [] ## [single_end, fq1, fq2, strandedness] + if sample and fq1 and fq2: ## Paired-end short reads + sample_info = ["0", fq1, fq2, strandedness] + elif sample and fq1 and not fq2: ## Single-end short reads + sample_info = ["1", fq1, fq2, strandedness] + else: + print_error("Invalid combination of columns provided!", "Line", line) + + ## Create sample mapping dictionary = {sample: [[ single_end, fq1, fq2, strandedness ]]} + if sample not in sample_mapping_dict: + sample_mapping_dict[sample] = [sample_info] + else: + if sample_info in sample_mapping_dict[sample]: + print_error("Samplesheet contains duplicate rows!", "Line", line) + else: + sample_mapping_dict[sample].append(sample_info) + + ## Write validated samplesheet with appropriate columns + if len(sample_mapping_dict) > 0: + out_dir = os.path.dirname(file_out) + make_dir(out_dir) + with open(file_out, "w") as fout: + fout.write( + ",".join(["sample", "single_end", "fq1", "fq2", "strandedness"]) + + "\n" + ) + for sample in sorted(sample_mapping_dict.keys()): + + ## Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end + if not all( + x[0] == sample_mapping_dict[sample][0][0] + for x in sample_mapping_dict[sample] + ): + print_error( + f"Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end!", + "Sample", + sample, + ) + + ## Check that multiple runs of the same sample are of the same strandedness + if not all( + x[-1] == sample_mapping_dict[sample][0][-1] + for x in sample_mapping_dict[sample] + ): + print_error( + f"Multiple runs of a sample must have the same strandedness!", + "Sample", + sample, + ) + + for idx, val in enumerate(sample_mapping_dict[sample]): + fout.write(",".join([f"{sample}_T{idx+1}"] + val) + "\n") + else: + print_error(f"No entries to process!", "Samplesheet: {file_in}") + + +def main(args=None): + args = parse_args(args) + check_samplesheet(args.FILE_IN, args.FILE_OUT) + + +if __name__ == "__main__": + sys.exit(main())
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/bin/create_mqc_data_table.py Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,124 @@ +#!/usr/bin/env python + +import sys +import yaml +from textwrap import dedent + +def main() : + """ + Takes a tab-delimited text file with a mandatory header + column and generates an HTML table. + """ + + args = sys.argv + if (len(args) < 2 or len(args) > 3): + print(f"\nTwo CL arguments are required!\n") + exit(1) + + table_sum_on = args[1].lower() + workflow_name = args[2].lower() + + with open(f"{table_sum_on}.tblsum.txt", "r") as tbl: + header = tbl.readline() + header_cols = header.strip().split('\t') + + html = [ + dedent( + f"""<script type="text/javascript"> + $(document).ready(function () {{ + $('#cpipes-process-custom-res-{table_sum_on}').DataTable({{ + scrollX: true, + fixedColumns: true, dom: 'Bfrtip', + buttons: [ + 'copy', + {{ + extend: 'print', + title: 'CPIPES: MultiQC Report: {table_sum_on}' + }}, + {{ + extend: 'excel', + filename: '{table_sum_on}_results', + }}, + {{ + extend: 'csv', + filename: '{table_sum_on}_results', + }} + ] + }}); + }}); + </script> + <div class="table-responsive"> + <style> + #cpipes-process-custom-res tr:nth-child(even) {{ + background-color: #f2f2f2; + }} + </style> + <table class="table" style="width:100%" id="cpipes-process-custom-res-{table_sum_on}"> + <thead> + <tr>""" + ) + ] + + for header_col in header_cols: + html.append( + dedent( + f""" + <th> {header_col} </th>""" + ) + ) + + html.append( + dedent( + """ + </tr> + </thead> + <tbody>""" + ) + ) + + for row in tbl: + html.append("<tr>\n") + data_cols = row.strip().split('\t') + if ( len(header_cols) != len(data_cols) ): + print(f"\nWARN: Number of header columns ({len(header_cols)}) and data " + + f"columns ({len(data_cols)}) are not equal!\nWill append empty columns!\n") + if ( len(header_cols) > len(data_cols) ): + data_cols += (( len(header_cols) - len(data_cols) ) * ' ' ) + print(len(data_cols)) + else: + header_cols += (( len(data_cols) - len(header_cols) ) * ' ') + + html.append( + dedent( + f""" + <td><samp>{data_cols[0]}</samp></td> + """ + ) + ) + + for data_col in data_cols[1:]: + html.append( + dedent( + f"""<td>{data_col}</td> + """ + ) + ) + html.append("</tr>\n") + html.append("</tbody>\n") + html.append("</table>\n") + html.append("</div>\n") + + mqc_yaml = { + "id": f"{table_sum_on.upper()}_collated_table", + "section_name": f"{table_sum_on.upper()}", + "section_href": f"https://cfsan-git.fda.gov/Kranti.Konganti/{workflow_name}", + "plot_type": "html", + "description": "The results table shown here is a collection from all samples.", + "data": ('').join(html), + } + + with open(f"{table_sum_on.lower()}_mqc.yml", "w") as html_mqc: + yaml.dump(mqc_yaml, html_mqc, default_flow_style=False) + +if __name__ == "__main__": + main() \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/bin/extract_assembled_filtered_contigs.py Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,56 @@ +#!/usr/bin/env python + +import os +import argparse +import logging as log +import pandas as pd +import numpy as np +from Bio import SeqIO + + +def main(): + # READ IN ARGUMENTS + desc = """This script is part of the centriflaken pipeline: + - accepts assembled contigs (assembly.fasta from flye) and kraken classification (kraken_output.txt from kraken2) output + - filters the assembled contigs based on taxa specified + - outputs an assembled and filtered fasta (assembled_filtered_contigs.fasta) """ + parser = argparse.ArgumentParser(prog='extract_assembled_filtered_contigs.py', description=desc) + parser.add_argument("-v", dest='verbose', action="store_true", help="for more verbose output") + parser.add_argument("-i", dest='input_fasta', required=True, help="Path to input fasta file (assembled output from flye)") + parser.add_argument("-o", dest='assembled_filtered_contigs', required=True, help="Path to output fasta file filtered by taxa specified") + parser.add_argument("-k", dest='kraken_output', required=True, help="Path to kraken output file") + parser.add_argument("-b", dest='bug', required=True, help="name or fragment of name of bug") + args = parser.parse_args() + + # MORE INFO IF VERBOSE + if args.verbose: + log.basicConfig(format="%(levelname)s: %(message)s", level=log.DEBUG) + else: + log.basicConfig(format="%(levelname)s: %(message)s") + + # ASSIGN VARIABLES + input_fasta = args.input_fasta + assembled_filtered_contigs = args.assembled_filtered_contigs + kraken_output = args.kraken_output + bug = args.bug + + # Match and filter taxa names and ids from kraken output file + report_df = pd.read_csv(kraken_output, delimiter="\t", usecols=[1,2], header=None) + report_df.columns = ["contig", "name"] + report_df['name'] = report_df['name'].str.lower() + filt_report_df = report_df[report_df['name'].str.contains(bug.lower())] + print("\nMatching taxa names and ids:\n",filt_report_df) + filtered_contig_list = filt_report_df['contig'] + + # Extract filtered reads from assembled input fasta and write to output fasta + print ("Indexing reads..") + rec = SeqIO.index(input_fasta,"fasta") + TF=open(assembled_filtered_contigs, "w") + for i in filtered_contig_list: + if i in rec: + SeqIO.write(rec[i], TF, "fasta") + TF.close() + + +if __name__ == "__main__": + main() \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/bin/fastq_dir_to_samplesheet.py Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,177 @@ +#!/usr/bin/env python3 + +import os +import sys +import glob +import argparse +import re + + +def parse_args(args=None): + Description = "Generate samplesheet from a directory of FastQ files." + Epilog = "Example usage: python fastq_dir_to_samplesheet.py <FASTQ_DIR> <SAMPLESHEET_FILE>" + + parser = argparse.ArgumentParser(description=Description, epilog=Epilog) + parser.add_argument("FASTQ_DIR", help="Folder containing raw FastQ files.") + parser.add_argument("SAMPLESHEET_FILE", help="Output samplesheet file.") + parser.add_argument( + "-st", + "--strandedness", + type=str, + dest="STRANDEDNESS", + default="unstranded", + help="Value for 'strandedness' in samplesheet. Must be one of 'unstranded', 'forward', 'reverse'.", + ) + parser.add_argument( + "-r1", + "--read1_extension", + type=str, + dest="READ1_EXTENSION", + default="_R1_001.fastq.gz", + help="File extension for read 1.", + ) + parser.add_argument( + "-r2", + "--read2_extension", + type=str, + dest="READ2_EXTENSION", + default="_R2_001.fastq.gz", + help="File extension for read 2.", + ) + parser.add_argument( + "-se", + "--single_end", + dest="SINGLE_END", + action="store_true", + help="Single-end information will be auto-detected but this option forces paired-end FastQ files to be treated as single-end so only read 1 information is included in the samplesheet.", + ) + parser.add_argument( + "-sn", + "--sanitise_name", + dest="SANITISE_NAME", + action="store_true", + help="Whether to further sanitise FastQ file name to get sample id. Used in conjunction with --sanitise_name_delimiter and --sanitise_name_index.", + ) + parser.add_argument( + "-sd", + "--sanitise_name_delimiter", + type=str, + dest="SANITISE_NAME_DELIMITER", + default="_", + help="Delimiter to use to sanitise sample name.", + ) + parser.add_argument( + "-si", + "--sanitise_name_index", + type=int, + dest="SANITISE_NAME_INDEX", + default=1, + help="After splitting FastQ file name by --sanitise_name_delimiter all elements before this index (1-based) will be joined to create final sample name.", + ) + return parser.parse_args(args) + + +def fastq_dir_to_samplesheet( + fastq_dir, + samplesheet_file, + strandedness="unstranded", + read1_extension="_R1_001.fastq.gz", + read2_extension="_R2_001.fastq.gz", + single_end=False, + sanitise_name=False, + sanitise_name_delimiter="_", + sanitise_name_index=1, +): + def sanitize_sample(path, extension): + """Retrieve sample id from filename""" + sample = os.path.basename(path).replace(extension, "") + if sanitise_name: + if sanitise_name_index > 0: + sample = sanitise_name_delimiter.join( + os.path.basename(path).split(sanitise_name_delimiter)[ + :sanitise_name_index + ] + ) + # elif sanitise_name_index == -1: + # sample = os.path.basename(path)[ :os.path.basename(path).index('.') ] + return sample + + def get_fastqs(extension): + """ + Needs to be sorted to ensure R1 and R2 are in the same order + when merging technical replicates. Glob is not guaranteed to produce + sorted results. + See also https://stackoverflow.com/questions/6773584/how-is-pythons-glob-glob-ordered + """ + abs_fq_files = glob.glob(os.path.join(fastq_dir, f"**", f"*{extension}"), recursive=True) + return sorted( + [ + fq for _, fq in enumerate(abs_fq_files) if re.match('^((?!undetermined|unclassified|downloads).)*$', fq, flags=re.IGNORECASE) + ] + ) + + read_dict = {} + + ## Get read 1 files + for read1_file in get_fastqs(read1_extension): + sample = sanitize_sample(read1_file, read1_extension) + if sample not in read_dict: + read_dict[sample] = {"R1": [], "R2": []} + read_dict[sample]["R1"].append(read1_file) + + ## Get read 2 files + if not single_end: + for read2_file in get_fastqs(read2_extension): + sample = sanitize_sample(read2_file, read2_extension) + read_dict[sample]["R2"].append(read2_file) + + ## Write to file + if len(read_dict) > 0: + out_dir = os.path.dirname(samplesheet_file) + if out_dir and not os.path.exists(out_dir): + os.makedirs(out_dir) + + with open(samplesheet_file, "w") as fout: + header = ["sample", "fq1", "fq2", "strandedness"] + fout.write(",".join(header) + "\n") + for sample, reads in sorted(read_dict.items()): + for idx, read_1 in enumerate(reads["R1"]): + read_2 = "" + if idx < len(reads["R2"]): + read_2 = reads["R2"][idx] + sample_info = ",".join([sample, read_1, read_2, strandedness]) + fout.write(f"{sample_info}\n") + else: + error_str = ( + "\nWARNING: No FastQ files found so samplesheet has not been created!\n\n" + ) + error_str += "Please check the values provided for the:\n" + error_str += " - Path to the directory containing the FastQ files\n" + error_str += " - '--read1_extension' parameter\n" + error_str += " - '--read2_extension' parameter\n" + print(error_str) + sys.exit(1) + + +def main(args=None): + args = parse_args(args) + + strandedness = "unstranded" + if args.STRANDEDNESS in ["unstranded", "forward", "reverse"]: + strandedness = args.STRANDEDNESS + + fastq_dir_to_samplesheet( + fastq_dir=args.FASTQ_DIR, + samplesheet_file=args.SAMPLESHEET_FILE, + strandedness=strandedness, + read1_extension=args.READ1_EXTENSION, + read2_extension=args.READ2_EXTENSION, + single_end=args.SINGLE_END, + sanitise_name=args.SANITISE_NAME, + sanitise_name_delimiter=args.SANITISE_NAME_DELIMITER, + sanitise_name_index=args.SANITISE_NAME_INDEX, + ) + + +if __name__ == "__main__": + sys.exit(main())
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/bin/prepare_nanopore_fastq_dir.py Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,117 @@ +#!/usr/bin/env python3 + +import os +import re +import glob +import argparse +import logging + +def main(): + # READ IN ARGUMENTS + desc = """ + Takes in a file with flowcell ID, one per line and creates soft links + to 'fastq_pass' directory at target location. + + Ex: + + prepare_nanopore_fastq_dir.py \ + -o /hpc/scratch/Kranti.Konganti/np_test \ + -f flowcells.txt + + where flowcells.txt contains the following lines: + + FAL11127 + FAL11151 + + """ + parser = argparse.ArgumentParser(prog='prepare_nanopore_fastq_dir.py', + formatter_class=argparse.ArgumentDefaultsHelpFormatter, + description=desc) + required = parser.add_argument_group('required arguments') + + required.add_argument("-f", dest='flowcells', required=True, + help="Path to a text file containing Nanopore flowcell IDs, one per line") + required.add_argument("-i", dest='inputdir', + required=False, action='append', nargs='*', + help="Path to search directory. This directory location is where" + + " the presence of 'fastq_pass' will be searched for each flowcell.") + required.add_argument("-o", dest='outputdir', + required=True, + help="Path to output directory. This directory is created by the script" + + " and new soft links (symlinks) are created in this directory.") + + args = parser.parse_args() + flowcells = args.flowcells + output = args.outputdir + inputs = args.inputdir + + logging.basicConfig(format='%(asctime)s - %(levelname)s => %(message)s', level=logging.DEBUG) + + if not inputs: + inputs = ['/projects/nanopore/raw'] + nanopore_machines = ['RazorCrest', 'Revolution', 'ObiWan', 'MinIT', + 'Mayhem', 'CaptainMarvel', 'MinION', 'MinION_Padmini', 'RogueOne'] + logging.info(f"Searching default path(s). Use -i option if custom path should be searched.") + else: + nanopore_machines = ['custom'] + + fastq_pass_found = {} + was_fastq_pass_found = [] + + for each_input in inputs: + for machine in nanopore_machines: + if ''.join(nanopore_machines) != 'custom': + input = os.path.join(each_input, machine) + else: + input = ''.join(each_input) + + logging.info(f"Searching path: {input}") + + if (os.path.exists(flowcells) and os.path.getsize(flowcells) > 0): + with open(flowcells, 'r') as fcells: + for flowcell in fcells: + if re.match('^\s*$', flowcell): + continue + flowcell = flowcell.strip() + fastq_pass_path = glob.glob(os.path.join(input, flowcell, f"**", f"*[!fast5]*", 'fastq_pass')) + # Try one more time since the flowcell user is trying to query may be the parent directory + # of fastq_pass + fastq_pass = fastq_pass_path if fastq_pass_path else glob.glob(os.path.join(input, f"**", f"*[!fast5]*", flowcell, 'fastq_pass')) + if not fastq_pass: + # logging.warning(f"Flowcell " + + # os.path.join(input, flowcell).strip() + + # f" does not seem to have a fastq_pass directory! Skipped!!") + if not flowcell in fastq_pass_found.keys(): + fastq_pass_found[flowcell] = 0 + else: + fastq_pass_found[flowcell] = 1 + sym_link_dir = os.path.join(output, flowcell) + sym_link_dir_dest = os.path.join(sym_link_dir, 'fastq_pass') + if not os.path.exists(sym_link_dir): + os.makedirs(sym_link_dir) + os.symlink( + ''.join(fastq_pass), + sym_link_dir_dest, target_is_directory=True + ) + logging.info(f"New soft link created: {sym_link_dir_dest}") + else: + logging.info(f"Soft link {sym_link_dir_dest} already exists! Skipped!!") + fcells.close() + else: + logging.error(f"File {flowcells} is empty or does not exist!\n") + + for k,v in fastq_pass_found.items(): + if not v: + was_fastq_pass_found.append(k) + + if was_fastq_pass_found: + logging.warning("Did not find fastq_pass folder for the supplied flowcells: " + + ', '.join(was_fastq_pass_found)) + + if was_fastq_pass_found and len(was_fastq_pass_found) == len(fastq_pass_found): + logging.error(f"None of the supplied flowcells were found! The output directory, {output} may not have been created!") + else: + logging.info(f"NOTE: Now you can use {output} directory as --input to cpipes.\n") + +if __name__ == "__main__": + main() \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/bin/process_centrifuge_output.py Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,75 @@ +#!/usr/bin/env python + +import os +import argparse +import logging as log +import pandas as pd +import numpy as np +from Bio import SeqIO + + +def main(): + # READ IN ARGUMENTS + desc = """ + This script is part of the centriflaken pipeline: It processes centrifuge + output and produces either a filtered FASTQ or a text file of FASTQ IDs based + on the supplied taxa/bug + """ + parser = argparse.ArgumentParser(prog='process_centrifuge_output.py', description=desc) + parser.add_argument("-v", dest='verbose', action="store_true", help="For more verbose output") + parser.add_argument("-i", dest='input_fastq', required=False, + help="Path to input FASTQ file (same as input to centrifuge). If not mentioned, \ + a text file of sequence IDs are produced instead of a FASTQ file") + parser.add_argument("-t", dest='taxa_filtered_fastq_file', required=True, + help="Path to output FASTQ or output text file filtered by the taxa specified") + parser.add_argument("-r", dest='cent_report', required=True, help="Path to centrifuge report") + parser.add_argument("-o", dest='cent_output', required=True, help="Path to centrifuge output") + parser.add_argument("-b", dest='bug', required=True, + help="Name or fragment of name of the bug by which reads are extracted") + args = parser.parse_args() + + # MORE INFO IF VERBOSE + if args.verbose: + log.basicConfig(format="%(levelname)s: %(message)s", level=log.DEBUG) + else: + log.basicConfig(format="%(levelname)s: %(message)s") + + # ASSIGN VARIABLES + input_fastq = args.input_fastq + taxa_filtered_fastq_file = args.taxa_filtered_fastq_file + cent_report = args.cent_report + cent_output = args.cent_output + bug = args.bug + report_col_list = ["name", "taxID"] + output_col_list = ["taxID", "readID"] + + # Match and filter taxa names and ids from centrifuge report file + report_df = pd.read_csv(cent_report, delimiter="\t", usecols=report_col_list) + report_df['name'] = report_df['name'].str.lower() + filt_report_df = report_df[report_df['name'].str.contains(bug.lower())] + #print("\nMatching taxa names and ids:\n",filt_report_df) + taxID_list = filt_report_df['taxID'] + + # Match the above tax ids to read ids from centrifuge output file and deduplicate + output_df = pd.read_csv(cent_output, delimiter="\t", usecols=output_col_list) + filt_output_df = output_df.loc[output_df['taxID'].isin(taxID_list)] + readID_list = filt_output_df['readID'] + readID_dedup_list = np.unique(readID_list) + TF=open(taxa_filtered_fastq_file, "w") + + if (not input_fastq): + # print("\nFILTERED READ ID LIST:\n", readID_dedup_list) + for ID in readID_dedup_list: + TF.write(f"{ID}\n") + else: + # Extract filtered reads from input fastq and write to output fastq + print ("Indexing reads..") + rec = SeqIO.index(input_fastq,"fastq") + for i in readID_dedup_list: + if i in rec: + SeqIO.write(rec[i], TF, "fastq") + + TF.close() + +if __name__ == "__main__": + main() \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/conf/base.config Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,52 @@ +params { + fs = File.separator + cfsanpipename = 'CPIPES' + center = 'CFSAN, FDA.' + libs = "${projectDir}${params.fs}lib" + modules = "${projectDir}${params.fs}modules" + projectconf = "${projectDir}${params.fs}conf" + assetsdir = "${projectDir}${params.fs}assets" + subworkflows = "${projectDir}${params.fs}subworkflows" + workflows = "${projectDir}${params.fs}workflows" + workflowsconf = "${workflows}${params.fs}conf" + routines = "${libs}${params.fs}routines" + toolshelp = "${libs}${params.fs}help" + swmodulepath = "${params.fs}nfs${params.fs}software${params.fs}modules" + tracereportsdir = "${launchDir}${params.fs}${cfsanpipename}-${params.pipeline}${params.fs}nextflow-reports" + dummyfile = "${projectDir}${params.fs}assets${params.fs}dummy_file.txt" + dummyfile2 = "${projectDir}${params.fs}assets${params.fs}dummy_file2.txt" + linewidth = 80 + pad = 32 + pipeline = null + help = null + input = null + output = null + metadata = null + publish_dir_mode = "copy" + publish_dir_overwrite = true + user_email = null +} + +dag { + enabled = true + file = "${params.tracereportsdir}${params.fs}${params.pipeline}_dag.html" + overwrite = true +} + +report { + enabled = true + file = "${params.tracereportsdir}${params.fs}${params.pipeline}_exec_report.html" + overwrite = true +} + +trace { + enabled = true + file = "${params.tracereportsdir}${params.fs}${params.pipeline}_exec_trace.txt" + overwrite = true +} + +timeline { + enabled = true + file = "${params.tracereportsdir}${params.fs}${params.pipeline}_exec_timeline.html" + overwrite = true +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/conf/computeinfra.config Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,155 @@ +standard { + process.executor = 'local' + process.cpus = 1 + params.enable_conda = false + params.enable_module = true + singularity.enabled = false + docker.enabled = false +} + +stdkondagac { + process.executor = 'local' + process.cpus = 4 + params.enable_conda = true + conda.enabled = true + conda.useMicromamba = true + params.enable_module = false + singularity.enabled = false + docker.enabled = false +} + +stdcingularitygac { + process.executor = 'local' + process.cpus = 4 + params.enable_conda = false + params.enable_module = false + singularity.enabled = true + singularity.autoMounts = true + singularity.runOptions = "-B ${params.input} -B ${params.bcs_root_dbdir}" + docker.enabled = false +} + +raven { + process.executor = 'slurm' + process.queue = 'prod' + process.memory = '10GB' + process.cpus = 4 + params.enable_conda = false + params.enable_module = true + singularity.enabled = false + docker.enabled = false + clusterOptions = '--signal B:USR2' +} + +eprod { + process.executor = 'slurm' + process.queue = 'combined' + process.memory = '10GB' + process.cpus = 4 + params.enable_conda = false + params.enable_module = true + singularity.enabled = false + docker.enabled = false + clusterOptions = '--signal B:USR2' +} + +eprodkonda { + process.executor = 'slurm' + process.queue = 'combined' + process.memory = '10GB' + process.cpus = 4 + params.enable_conda = true + conda.enabled = true + conda.useMicromamba = true + params.enable_module = false + singularity.enabled = false + singularity.autoMounts = true + singularity.runOptions = "-B ${params.input} -B ${params.bcs_root_dbdir}" + docker.enabled = false + clusterOptions = '--signal B:USR2' +} + +eprodcingularity { + process.executor = 'slurm' + process.queue = 'combined' + process.memory = '10GB' + process.cpus = 4 + params.enable_conda = false + params.enable_module = false + singularity.enabled = true + singularity.autoMounts = true + singularity.runOptions = "-B ${params.input} -B ${params.bcs_root_dbdir}" + docker.enabled = false + clusterOptions = '--signal B:USR2' +} + +cingularity { + process.executor = 'slurm' + process.queue = 'prod' + process.memory = '10GB' + process.cpus = 4 + singularity.enabled = true + singularity.autoMounts = true + singularity.runOptions = "-B ${params.input} -B ${params.bcs_root_dbdir}" + docker.enabled = false + params.enable_conda = false + params.enable_module = false + clusterOptions = '--signal B:USR2' +} + +cingularitygac { + process.executor = 'slurm' + executor.$slurm.exitReadTimeout = 120000 + process.queue = 'centriflaken' + process.cpus = 4 + singularity.enabled = true + singularity.autoMounts = true + singularity.runOptions = "-B ${params.input} -B ${params.bcs_root_dbdir}" + docker.enabled = false + params.enable_conda = false + params.enable_module = false + clusterOptions = '-n 1 --signal B:USR2' +} + +konda { + process.executor = 'slurm' + process.queue = 'prod' + process.memory = '10GB' + process.cpus = 4 + singularity.enabled = false + docker.enabled = false + params.enable_conda = true + conda.enabled = true + conda.useMicromamba = true + params.enable_module = false + clusterOptions = '--signal B:USR2' +} + +kondagac { + process.executor = 'slurm' + executor.$slurm.exitReadTimeout = 120000 + process.queue = 'centriflaken' + process.cpus = 4 + singularity.enabled = false + docker.enabled = false + params.enable_conda = true + conda.enabled = true + conda.useMicromamba = true + params.enable_module = false + clusterOptions = '-n 1 --signal B:USR2' +} + +cfsanawsbatch { + process.executor = 'awsbatch' + process.queue = 'cfsan-nf-batch-job-queue' + aws.batch.cliPath = '/home/ec2-user/miniconda/bin/aws' + aws.batch.region = 'us-east-1' + aws.batch.volumes = ['/hpc/db:/hpc/db:ro', '/hpc/scratch:/hpc/scratch:rw'] + singularity.enabled = false + singularity.autoMounts = true + docker.enabled = true + params.enable_conda = false + conda.enabled = false + conda.useMicromamba = false + params.enable_module = false +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/conf/fastq.config Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,9 @@ +params { + fq_filter_by_len = "4000" + fq_suffix = ".fastq.gz" + fq2_suffix = false + fq_strandedness = "unstranded" + fq_single_end = false + fq_filename_delim = "_" + fq_filename_delim_idx = "1" +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/conf/logtheseparams.config Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,16 @@ +params { + logtheseparams = [ + "${params.metadata}" ? 'metadata' : null, + "${params.input}" ? 'input' : null, + "${params.output}" ? 'output' : null, + "${params.fq_suffix}" ? 'fq_suffix' : null, + "${params.fq2_suffix}" ? 'fq2_suffix' : null, + "${params.fq_strandedness}" ? 'fq_strandedness' : null, + "${params.fq_single_end}" ? 'fq_single_end' : null, + "${params.fq_filter_by_len}" ? 'fq_filter_by_len' : null, + "${params.fq_filename_delim}" ? 'fq_filename_delim' : null, + "${params.fq_filename_delim_idx}" ? 'fq_filename_delim_idx' : null, + 'enable_conda', + 'enable_module', + ] +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/conf/manifest.config Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,8 @@ +manifest { + author = 'Kranti.Konganti@fda.hhs.gov' + homePage = 'https://cfsan-git.fda.gov/cfsan-dev/cpipes' + name = 'CPIPES' + version = '0.4.1' + nextflowVersion = '>=21.12' + description = 'Modular Nextflow pipelines at CFSAN, FDA.' +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/conf/modules.config Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,111 @@ +process { + publishDir = [ + path: { + "${task.process.tokenize(':')[-1].toLowerCase()}" == "multiqc" ? + "${params.output}${params.fs}${params.pipeline.toLowerCase()}-${task.process.tokenize(':')[-1].toLowerCase()}" : + "${params.output}${params.fs}${task.process.tokenize(':')[-1].toLowerCase()}" + }, + mode: params.publish_dir_mode, + overwrite: params.publish_dir_overwrite, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + + errorStrategy = { + ![0].contains(task.exitStatus) ? dynamic_retry(task.attempt, 10) : 'finish' + } + + maxRetries = 1 + + withLabel: 'process_femto' { + cpus = { 1 * task.attempt } + memory = { 1.GB * task.attempt } + time = { 1.h * task.attempt } + } + + withLabel: 'process_pico' { + cpus = { 2 * task.attempt } + memory = { 4.GB * task.attempt } + time = { 2.h * task.attempt } + } + + withLabel: 'process_nano' { + cpus = { 4 * task.attempt } + memory = { 8.GB * task.attempt } + time = { 4.h * task.attempt } + } + + withLabel: 'process_micro' { + cpus = { 8 * task.attempt } + memory = { 16.GB * task.attempt } + time = { 8.h * task.attempt } + } + + withLabel: 'process_only_mem_low' { + cpus = { 1 * task.attempt } + memory = { 60.GB * task.attempt } + time = { 20.h * task.attempt } + } + + withLabel: 'process_only_mem_medium' { + cpus = { 1 * task.attempt } + memory = { 100.GB * task.attempt } + time = { 30.h * task.attempt } + } + + withLabel: 'process_only_mem_high' { + cpus = { 1 * task.attempt } + memory = { 128.GB * task.attempt } + time = { 60.h * task.attempt } + } + + withLabel: 'process_low' { + cpus = { 10 * task.attempt } + memory = { 60.GB * task.attempt } + time = { 20.h * task.attempt } + } + + withLabel: 'process_medium' { + cpus = { 10 * task.attempt } + memory = { 100.GB * task.attempt } + time = { 30.h * task.attempt } + } + + withLabel: 'process_high' { + cpus = { 10 * task.attempt } + memory = { 128.GB * task.attempt } + time = { 60.h * task.attempt } + } + + withLabel: 'process_higher' { + cpus = { 10 * task.attempt } + memory = { 256.GB * task.attempt } + time = { 60.h * task.attempt } + } + + withLabel: 'process_gigantic' { + cpus = { 10 * task.attempt } + memory = { 512.GB * task.attempt } + time = { 60.h * task.attempt } + } +} + +if ( (params.input || params.metadata ) && params.pipeline ) { + try { + includeConfig "${params.workflowsconf}${params.fs}process${params.fs}${params.pipeline}.process.config" + } catch (Exception e) { + System.err.println('-'.multiply(params.linewidth) + "\n" + + "\033[0;31m${params.cfsanpipename} - ERROR\033[0m\n" + + '-'.multiply(params.linewidth) + "\n" + "\033[0;31mCould not load " + + "default pipeline's process configuration. Please provide a pipeline \n" + + "name using the --pipeline option.\n\033[0m" + '-'.multiply(params.linewidth) + "\n") + System.exit(1) + } +} + +// Function will return after sleeping for some time. +// Sleep time increases exponentially by task attempt. +def dynamic_retry(task_retry_num, factor_by) { + // sleep(Math.pow(2, task_retry_num.toInteger()) * factor_by.toInteger() as long) + sleep(Math.pow(1.27, task_retry_num.toInteger()) as long) + return 'retry' +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/conf/multiqc/centriflaken_hy_mqc.yml Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,82 @@ +custom_logo: "FDa-Logo-Blue---medium-01.png" +custom_logo_url: "https://www.fda.gov/about-fda/fda-organization/center-food-safety-and-applied-nutrition-cfsan" +custom_logo_title: "CFSAN, FDA" +title: CPIPES Report +intro_text: > + CPIPES is a modular bioinformatics data analysis project at HFP, FDA based on NEXTFLOW DSL2. +report_comment: > + This report has been generated by the <a href="https://cfsan-git.fda.gov/Kranti.Konganti/cpipes/blob/master/readme/Workflow_Name_Placeholder.md" target="_blank">CPIPES - Workflow_Name_Placeholder</a> + analysis pipeline. Only certain tables and plots are reported here. For complete results, please refer to the analysis pipeline output directory. +report_header_info: + - CPIPES Version: CPIPES_Version_Placeholder + - Workflow: Workflow_Name_Placeholder + - Workflow Version: Workflow_Version_Placeholder + - Input Directory: Workflow_Input_Placeholder + - Output Directory: Workflow_Output_Placeholder + - Developer E-mail: "Kranti.Konganti@fda.hhs.gov" + - Stakeholder E-mail: "Narjol.Gonzalez-Escalona@fda.hhs.gov" +show_analysis_paths: False +show_analysis_time: False +report_section_order: + MLST_collated_table: + order: -989 + ECTYPER_collated_table: + order: -990 + SEROTYPEFINDER_collated_table: + order: -991 + SEQSERO2_collated_table: + order: -992 + ABRICATE_ECOLI_VF_collated_table: + order: -993 + ABRICATE_NCBI_collated_table: + order: -994 + ABRICATE_NCBIAMRPLUS_collated_table: + order: -995 + ABRICATE_MEGARES_collated_table: + order: -996 + ABRICATE_RESFINDER_collated_table: + order: -997 + ABRICATE_ARGANNOT_collated_table: + order: -998 + software_versions: + order: -999 + +export_plots: true + +# Run only these modules +run_modules: + - fastqc + - kraken + - custom_content + +module_order: + - fastqc: + name: "FastQC" + info: "section of the report shows FastQC results <b>before</b> adapter trimming." + path_filters: + - "*_fastqc.zip" + - kraken: + name: "Centrifuge" + href: "https://ccb.jhu.edu/software/centrifuge" + doi: "10.1101/gr.210641.116" + info: > + section of the report shows how <b>reads</b> are classified. + Please note that the plot title below is shown as + <b>Kraken2: Top taxa</b> since <code>centrifuge-kreport</code> was used + to create Kraken-style reports from centrifuge output files. + path_filters: + - "*.kreport.txt" + - kraken: + name: "Kraken2" + info: "section of the report shows how <b>assembled contigs</b> are classified." + path_filters: + - "*.report.txt" + +extra_fn_clean_exts: + - ".centrifuge.kreport" + - ".report" + +table_columns_visible: + Kraken: False + Kraken2: False + Centrifuge: False
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/conf/multiqc/centriflaken_mqc.yml Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,77 @@ +title: CPIPES Report +intro_text: > + CPIPES is a modular bioinformatics data analysis project at HFP, FDA based on NEXTFLOW DSL2. +report_comment: > + This report has been generated by the <a href="https://github.com/CFSAN-Biostatistics/centriflaken" target="_blank">CPIPES - Workflow_Name_Placeholder</a> + analysis pipeline. Only certain tables and plots are reported here. For complete results, please refer to the analysis pipeline output directory. +report_header_info: + - CPIPES Version: CPIPES_Version_Placeholder + - Workflow: Workflow_Name_Placeholder + - Workflow Version: Workflow_Version_Placeholder + - Input Directory: Workflow_Input_Placeholder + - Output Directory: Workflow_Output_Placeholder +show_analysis_paths: False +show_analysis_time: False +report_section_order: + MLST_collated_table: + order: -989 + ECTYPER_collated_table: + order: -990 + SEROTYPEFINDER_collated_table: + order: -991 + SEQSERO2_collated_table: + order: -992 + ABRICATE_ECOLI_VF_collated_table: + order: -993 + ABRICATE_NCBI_collated_table: + order: -994 + ABRICATE_NCBIAMRPLUS_collated_table: + order: -995 + ABRICATE_MEGARES_collated_table: + order: -996 + ABRICATE_RESFINDER_collated_table: + order: -997 + ABRICATE_ARGANNOT_collated_table: + order: -998 + software_versions: + order: -999 + +export_plots: true + +# Run only these modules +run_modules: + - fastqc + - kraken + - custom_content + +module_order: + - fastqc: + name: "FastQC" + info: "section of the report shows FastQC results <b>before</b> adapter trimming." + path_filters: + - "*_fastqc.zip" + - kraken: + name: "Centrifuge" + href: "https://ccb.jhu.edu/software/centrifuge" + doi: "10.1101/gr.210641.116" + info: > + section of the report shows how <b>reads</b> are classified. + Please note that the plot title below is shown as + <b>Kraken2: Top taxa</b> since <code>centrifuge-kreport</code> was used + to create Kraken-style reports from centrifuge output files. + path_filters: + - "*.kreport.txt" + - kraken: + name: "Kraken2" + info: "section of the report shows how <b>assembled contigs</b> are classified." + path_filters: + - "*.report.txt" + +extra_fn_clean_exts: + - ".centrifuge.kreport" + - ".report" + +table_columns_visible: + Kraken: False + Kraken2: False + Centrifuge: False
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/cpipes Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,68 @@ +#!/usr/bin/env nextflow + +/* +---------------------------------------------------------------------------------------- + cpipes/centriflaken +---------------------------------------------------------------------------------------- + NAME : CPIPES + DESCRIPTION : Modular Nextflow pipelines at CFSAN, FDA. + GITLAB : https://xxxxxxxxxx.fda.gov/cfsan-dev/cpipes + JIRA : https://xxxxxxxxxx.fda.gov/jira/projects/CPIPES/ + CONTRIBUTORS : Kranti.Konganti@fda.hhs.gov +---------------------------------------------------------------------------------------- +*/ + +// Enable DSL 2 +nextflow.enable.dsl = 2 + +// Default routines for MAIN +include { pipelineBanner; stopNow; } from "${params.routines}" + +// Our banner for CPIPES +log.info pipelineBanner() + +switch ("${params.pipeline}") { + case "nanofactory": + include { NANOFACTORY } from "${params.workflows}${params.fs}${params.pipeline}" + break + case "centriflaken": + include { CENTRIFLAKEN } from "${params.workflows}${params.fs}${params.pipeline}" + break + case "centriflaken_hy": + include { CENTRIFLAKEN_HY } from "${params.workflows}${params.fs}${params.pipeline}" + break + case "spades_only": + include { SPADES_ONLY } from "${params.workflows}${params.fs}${params.pipeline}" + break + default: + stopNow("PLEASE MENTION A PIPELINE NAME. Ex: --pipeline centriflaken") +} + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + RUN ALL WORKFLOWS +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +workflow { + switch ("${params.pipeline}") { + case "nanofactory": + NANOFACTORY() + break + case "centriflaken": + CENTRIFLAKEN() + break + case "centriflaken_hy": + CENTRIFLAKEN_HY() + break + case "spades_only": + SPADES_ONLY() + break + } +} + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + THE END +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/lib/help/abricate.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,43 @@ +// Help text for abricate within CPIPES. + +def abricateHelp(params) { + +Map tool = [:] +Map toolspecs = [:] +tool.text = [:] +tool.helpparams = [:] + + toolspecs = [ + 'abricate_run': [ + clihelp: 'Run ABRicate tool. Default: ' + + (params.abricate_run ?: false), + cliflag: null, + clivalue: null + ], + 'abricate_minid': [ + clihelp: 'Minimum DNA %identity. ' + + "Defaut: " + (params.abricate_minid ?: 80), + cliflag: '--minid', + clivalue: (params.abricate_minid ?: 80) + ], + 'abricate_mincov': [ + clihelp: 'Minimum DNA %coverage. ' + + "Defaut: " + (params.abricate_mincov ?: 80), + cliflag: '--mincov', + clivalue: (params.abricate_mincov ?: 80) + ], + 'abricate_datadir': [ + clihelp: 'ABRicate databases folder. ' + + "Defaut: " + (params.abricate_datadir ?: 'undefined'), + cliflag: '--datadir', + clivalue: (params.abricate_datadir ?: '') + ] + ] + + toolspecs.each { + k, v -> tool.text['--' + k] = "${v.clihelp}" + tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ] + } + + return tool +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/lib/help/amrfinderplus.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,36 @@ +def amrfinderplusHelp(params) { + + Map tool = [:] + Map toolspecs = [:] + tool.text = [:] + tool.helpparams = [:] + + toolspecs = [ + 'amrfinderplus_run': [ + clihelp: "Run AMRFinderPlus tool. Default: ${params.amrfinderplus_run}", + cliflag: null, + clivalue: null + ], + 'amrfinderplus_db': [ + clihelp: 'Path to AMRFinderPlus database. Please note that ' + + ' the databases should be ready and formatted with blast for use. ' + + 'Please read more at: ' + + 'https://github.com/ncbi/amr/wiki/AMRFinderPlus-database ' + + "Default: ${params.amrfinderplus_db}", + cliflag: '--database', + clivalue: (params.amrfinderplus_db ?: '') + ], + 'amrfinderplus_genes': [ + clihelp: 'Add the plus genes to the report', + cliflag: '--plus', + clivalue: (params.amrfinderplus_genes ? ' ' : '') + ] + ] + + toolspecs.each { + k, v -> tool.text['--' + k] = "${v.clihelp}" + tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ] + } + + return tool +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/lib/help/centrifuge.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,54 @@ +// Help text for centrifuge within CPIPES. + +def centrifugeHelp(params) { + + Map tool = [:] + Map toolspecs = [:] + tool.text = [:] + tool.helpparams = [:] + + toolspecs = [ + 'centrifuge_x': [ + clihelp: "Absolute path to centrifuge database. Default: ${params.centrifuge_x}", + cliflag: '-x', + clivalue: null + ], + 'centrifuge_save_unaligned': [ + clihelp: 'Save SINGLE-END reads that did not align. For PAIRED-END' + + " reads, save read pairs that did not align concordantly. Default: ${params.centrifuge_save_unaligned}", + cliflag: null, // Handled in modules logic. + clivalue: null + ], + 'centrifuge_save_aligned': [ + clihelp: 'Save SINGLE-END reads that aligned. For PAIRED-END' + + " reads, save read pairs that aligned concordantly. Default: ${params.centrifuge_save_aligned}", + cliflag: null, // Handled in modules logic. + clivalue: null + ], + 'centrifuge_out_fmt_sam': [ + clihelp: "Centrifuge output should be in SAM. Default: ${params.centrifuge_save_aligned}", + cliflag: null, // Handled in modules logic. + clivalue: null + ], + 'centrifuge_extract_bug': [ + clihelp: "Extract this bug from centrifuge results." + + " Default: ${params.centrifuge_extract_bug}", + cliflag: null, // Handled in modules logic. + clivalue: null, + ], + 'centrifuge_ignore_quals': [ + clihelp: 'Treat all quality values as 30 on Phred scale. ' + + "Default: ${params.centrifuge_ignore_quals}", + cliflag: '--ignore-quals', + clivalue: (params.centrifuge_ignore_quals ? ' ' : '') + ] + ] + + toolspecs.each { + k, v -> tool.text['--' + k] = "${v.clihelp}" + tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ] + } + + return tool +} +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/lib/help/ectyper.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,46 @@ +def ectyperHelp(params) { + + Map tool = [:] + Map toolspecs = [:] + tool.text = [:] + tool.helpparams = [:] + + toolspecs = [ + 'ectyper_run': [ + clihelp: "Run ectyper tool. Default: ${params.ectyper_run}", + cliflag: null, + clivalue: null + ], + 'ectyper_perc_opid': [ + clihelp: 'Percent identity required for an O antigen allele match. ' + + "Default: ${params.ectyper_perc_opid}", + cliflag: '-opid', + clivalue: (params.ectyper_perc_opid ?: 90) + ], + 'ectyper_perc_hpid': [ + clihelp: 'Percent identity required for a H antigen allele match. ' + + "Default: ${params.ectyper_perc_hpid}", + cliflag: '-hpid', + clivalue: (params.ectyper_perc_hpid ?: 95) + ], + 'ectyper_perc_opcov': [ + clihelp: 'Minumum percent coverage required for an O antigen allele match. ' + + "Default: ${params.ectyper_perc_opcov}", + cliflag: '-opcov', + clivalue: (params.ectyper_perc_opcov ?: 95) + ], + 'ectyper_perc_hpcov': [ + clihelp: 'Minumum percent coverage required for a H antigen allele match. ' + + "Default: ${params.ectyper_perc_hpcov}", + cliflag: '-hpcov', + clivalue: (params.ectyper_perc_hpcov ?: 50) + ] + ] + + toolspecs.each { + k, v -> tool.text['--' + k] = "${v.clihelp}" + tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ] + } + + return tool +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/lib/help/flye.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,82 @@ +// Help text for flye within CPIPES. + +def flyeHelp(params) { + +Map tool = [:] +Map toolspecs = [:] +tool.text = [:] +tool.helpparams = [:] + + toolspecs = [ + 'flye_pacbio_raw': [ + clihelp: 'Input FASTQ reads are PacBio regular CLR reads (<20% error) ' + + "Defaut: ${params.flye_pacbio_raw}", + cliflag: '--pacbio-raw', + clivalue: (params.flye_pacbio_raw ? ' ' : '') + ], + 'flye_pacbio_corr': [ + clihelp: 'Input FASTQ reads are PacBio reads that were corrected ' + + "with other methods (<3% error). Default: ${params.flye_pacbio_corr}", + cliflag: '--pacbio-corr', + clivalue: (params.flye_pacbio_corr ? ' ' : '') + ], + 'flye_pacbio_hifi': [ + clihelp: 'Input FASTQ reads are PacBio HiFi reads (<1% error). ' + + "Default: ${params.flye_pacbio_hifi}", + cliflag: '--pacbio-hifi', + clivalue: (params.flye_pacbio_hifi ? ' ' : '') + ], + 'flye_nano_raw': [ + clihelp: 'Input FASTQ reads are ONT regular reads, pre-Guppy5 (<20% error). ' + + "Default: ${params.flye_nano_raw}", + cliflag: '--nano-raw', + clivalue: (params.flye_nano_raw ? ' ' : '') + ], + 'flye_nano_corr': [ + clihelp: 'Input FASTQ reads are ONT reads that were corrected with other ' + + "methods (<3% error). Default: ${params.flye_nano_corr}", + cliflag: '--nano-corr', + clivalue: (params.flye_nano_corr ? ' ' : '') + ], + 'flye_nano_hq': [ + clihelp: 'Input FASTQ reads are ONT high-quality reads: ' + + "Guppy5+ SUP or Q20 (<5% error). Default: ${params.flye_nano_hq}", + cliflag: '--nano-hq', + clivalue: (params.flye_nano_hq ? ' ' : '') + ], + 'flye_genome_size': [ + clihelp: 'Estimated genome size (for example, 5m or 2.6g). ' + + "Default: ${params.flye_genome_size}", + cliflag: '--genome-size', + clivalue: (params.flye_genome_size ?: '') + ], + 'flye_polish_iter': [ + clihelp: 'Number of genome polishing iterations. ' + + "Default: ${params.flye_polish_iter}", + cliflag: '--iterations', + clivalue: (params.flye_polish_iter ?: '') + ], + 'flye_meta': [ + clihelp: "Do a metagenome assembly (unenven coverage mode). Default: ${params.flye_meta}", + cliflag: '--meta', + clivalue: (params.flye_meta ? ' ' : '') + ], + 'flye_min_overlap': [ + clihelp: "Minimum overlap between reads. Default: ${params.flye_min_overlap}", + cliflag: '--min-overlap', + clivalue: (params.flye_min_overlap ?: '') + ], + 'flye_scaffold': [ + clihelp: "Enable scaffolding using assembly graph. Default: ${params.flye_scaffold}", + cliflag: '--scaffold', + clivalue: (params.flye_scaffold ? ' ' : '') + ] + ] + + toolspecs.each { + k, v -> tool.text['--' + k] = "${v.clihelp}" + tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ] + } + + return tool +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/lib/help/kraken2.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,72 @@ +// Help text for kraken2 within CPIPES. + +def kraken2Help(params) { + + Map tool = [:] + Map toolspecs = [:] + tool.text = [:] + tool.helpparams = [:] + + toolspecs = [ + 'kraken2_db': [ + clihelp: "Absolute path to kraken database. Default: ${params.kraken2_db}", + cliflag: '--db', + clivalue: null + ], + 'kraken2_confidence': [ + clihelp: 'Confidence score threshold which must be ' + + "between 0 and 1. Default: ${params.kraken2_confidence}", + cliflag: '--confidence', + clivalue: (params.kraken2_confidence ?: '') + ], + 'kraken2_quick': [ + clihelp: "Quick operation (use first hit or hits). Default: ${params.kraken2_quick}", + cliflag: '--quick', + clivalue: (params.kraken2_quick ? ' ' : '') + ], + 'kraken2_use_mpa_style': [ + clihelp: "Report output like Kraken 1's " + + "kraken-mpa-report. Default: ${params.kraken2_use_mpa_style}", + cliflag: '--use-mpa-style', + clivalue: (params.kraken2_use_mpa_style ? ' ' : '') + ], + 'kraken2_minimum_base_quality': [ + clihelp: 'Minimum base quality used in classification ' + + " which is only effective with FASTQ input. Default: ${params.kraken2_minimum_base_quality}", + cliflag: '--minimum-base-quality', + clivalue: (params.kraken2_minimum_base_quality ?: '') + ], + 'kraken2_report_zero_counts': [ + clihelp: 'Report counts for ALL taxa, even if counts are zero. ' + + "Default: ${params.kraken2_report_zero_counts}", + cliflag: '--report-zero-counts', + clivalue: (params.kraken2_report_zero_counts ? ' ' : '') + ], + 'kraken2_report_minmizer_data': [ + clihelp: 'Report minimizer and distinct minimizer count' + + ' information in addition to normal Kraken report. ' + + "Default: ${params.kraken2_report_minimizer_data}", + cliflag: '--report-minimizer-data', + clivalue: (params.kraken2_report_minimizer_data ? ' ' : '') + ], + 'kraken2_use_names': [ + clihelp: 'Print scientific names instead of just taxids. ' + + "Default: ${params.kraken2_use_names}", + cliflag: '--use-names', + clivalue: (params.kraken2_use_names ? ' ' : '') + ], + 'kraken2_extract_bug': [ + clihelp: 'Extract the reads or contigs beloging to this bug. ' + + "Default: ${params.kraken2_extract_bug}", + cliflag: null, + clivalue: null + ] + ] + + toolspecs.each { + k, v -> tool.text['--' + k] = "${v.clihelp}" + tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ] + } + + return tool +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/lib/help/megahit.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,113 @@ +// Help text for megahit within CPIPES. + +def megahitHelp(params) { + +Map tool = [:] +Map toolspecs = [:] +tool.text = [:] +tool.helpparams = [:] + + toolspecs = [ + 'megahit_run': [ + clihelp: 'Run MEGAHIT assembler. Default: ' + + (params.megahit_run ?: false), + cliflag: null, + clivalue: null + ], + 'megahit_min_count': [ + clihelp: '<int>. Minimum multiplicity for filtering (k_min+1)-mers. ' + + "Defaut: ${params.megahit_min_count}", + cliflag: '--min-count', + clivalue: (params.megahit_min_count ?: '') + ], + 'megahit_k_list': [ + clihelp: 'Comma-separated list of kmer size. All values must be odd, in ' + + "the range 15-255, increment should be <= 28. Ex: '21,29,39,59,79,99,119,141'. " + + "Default: ${params.megahit_k_list}", + cliflag: '--k-list', + clivalue: (params.megahit_k_list ?: '') + ], + 'megahit_no_mercy': [ + clihelp: 'Do not add mercy k-mers. ' + + "Default: ${params.megahit_no_mercy}", + cliflag: '--no-mercy', + clivalue: (params.megahit_no_mercy ? ' ' : '') + ], + 'megahit_bubble_level': [ + clihelp: '<int>. Intensity of bubble merging (0-2), 0 to disable. ' + + "Default: ${params.megahit_bubble_level}", + cliflag: '--bubble-level', + clivalue: (params.megahit_bubble_level ?: '') + ], + 'megahit_merge_level': [ + clihelp: '<l,s>. Merge complex bubbles of length <= l*kmer_size and ' + + "similarity >= s. Default: ${params.megahit_merge_level}", + cliflag: '--merge-level', + clivalue: (params.megahit_merge_level ?: '') + ], + 'megahit_prune_level': [ + clihelp: '<int>. Strength of low depth pruning (0-3). ' + + "Default: ${params.megahit_prune_level}", + cliflag: '--prune-level', + clivalue: (params.megahit_prune_level ?: '') + ], + 'megahit_prune_depth': [ + clihelp: '<int>. Remove unitigs with avg k-mer depth less than this value. ' + + "Default: ${params.megahit_prune_depth}", + cliflag: '--prune-depth', + clivalue: (params.megahit_prune_depth ?: '') + ], + 'megahit_low_local_ratio': [ + clihelp: '<float>. Ratio threshold to define low local coverage contigs. ' + + "Default: ${params.megahit_low_local_ratio}", + cliflag: '--low-local-ratio', + clivalue: (params.megahit_low_local_ratio ?: '') + ], + 'megahit_max_tip_len': [ + clihelp: '<int>. remove tips less than this value [<int> * k]. ' + + "Default: ${params.megahit_max_tip_len}", + cliflag: '--max-tip-len', + clivalue: (params.megahit_max_tip_len ?: '') + ], + 'megahit_no_local': [ + clihelp: 'Disable local assembly. ' + + "Default: ${params.megahit_no_local}", + cliflag: '--no-local', + clivalue: (params.megahit_no_local ? ' ' : '') + ], + 'megahit_kmin_1pass': [ + clihelp: 'Use 1pass mode to build SdBG of k_min. ' + + "Default: ${params.megahit_kmin_1pass}", + cliflag: '--kmin-1pass', + clivalue: (params.megahit_kmin_1pass ? ' ' : '') + ], + 'megahit_preset': [ + clihelp: '<str>. Override a group of parameters. Valid values are '+ + "meta-sensitive which enforces '--min-count 1 --k-list 21,29,39,49,...,129,141', " + + 'meta-large (large & complex metagenomes, like soil) which enforces ' + + "'--k-min 27 --k-max 127 --k-step 10'. " + + "Default: ${params.megahit_preset}", + cliflag: '--preset', + clivalue: (params.megahit_preset ?: '') + ], + 'megahit_mem_flag': [ + clihelp: '<int>. SdBG builder memory mode. 0: minimum; 1: moderate; 2: use all memory specified. ' + + "Default: ${params.megahit_mem_flag}", + cliflag: '--mem-flag', + clivalue: (params.megahit_mem_flag ?: '') + ], + 'megahit_min_contig_len': [ + clihelp: '<int>. Minimum length of contigs to output. ' + + "Default: ${params.megahit_min_contig_len}", + cliflag: '--use-gpu', + clivalue: (params.megahit_min_contig_len ?: '') + ] + ] + + toolspecs.each { + k, v -> tool.text['--' + k] = "${v.clihelp}" + tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ] + } + + return tool +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/lib/help/mlst.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,40 @@ +def mlstHelp(params) { + + Map tool = [:] + Map toolspecs = [:] + tool.text = [:] + tool.helpparams = [:] + + toolspecs = [ + 'mlst_run': [ + clihelp: "Run MLST tool. Default: ${params.mlst_run}", + cliflag: null, + clivalue: null + ], + 'mlst_minid': [ + clihelp: "DNA %identity of full allelle to consider 'similar' [~]. " + + "Default: ${params.mlst_minid}", + cliflag: '--minid', + clivalue: (params.mlst_minid ?: 95) + ], + 'mlst_mincov': [ + clihelp: 'DNA %cov to report partial allele at all [?].' + + "Default: ${params.mlst_mincov}", + cliflag: '--mincov', + clivalue: (params.mlst_mincov ?: 10) + ], + 'mlst_minscore': [ + clihelp: 'Minumum score out of 100 to match a scheme.' + + "Default: ${params.mlst_minscore}", + cliflag: '--minscore', + clivalue: (params.mlst_minscore ?: 50) + ] + ] + + toolspecs.each { + k, v -> tool.text['--' + k] = "${v.clihelp}" + tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ] + } + + return tool +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/lib/help/seqkitgrep.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,69 @@ +// Help text for seqkit grep within CPIPES. + +def seqkitgrepHelp(params) { + +Map tool = [:] +Map toolspecs = [:] +tool.text = [:] +tool.helpparams = [:] + + toolspecs = [ + 'seqkit_grep_n': [ + clihelp: 'Match by full name instead of just ID. ' + + "Defaut: " + (params.seqkit_grep_n ?: 'undefined'), + cliflag: '--seqkit_grep_n', + clivalue: (params.seqkit_grep_n ? ' ' : '') + ], + 'seqkit_grep_s': [ + clihelp: 'Search subseq on seq, both positive and negative ' + + 'strand are searched, and mismatch allowed using flag --seqkit_grep_m. ' + + "Defaut: " + (params.seqkit_grep_s ?: 'undefined'), + cliflag: '--seqkit_grep_s', + clivalue: (params.seqkit_grep_s ? ' ' : '') + ], + 'seqkit_grep_c': [ + clihelp: 'Input is circular genome ' + + "Defaut: " + (params.seqkit_grep_c ?: 'undefined'), + cliflag: '--seqkit_grep_c', + clivalue: (params.seqkit_grep_c ? ' ' : '') + ], + 'seqkit_grep_C': [ + clihelp: 'Just print a count of matching records. With the ' + + '--seqkit_grep_v flag, count non-matching records. ' + + "Defaut: " + (params.seqkit_grep_v ?: 'undefined'), + cliflag: '--seqkit_grep_v', + clivalue: (params.seqkit_grep_v ? ' ' : '') + ], + 'seqkit_grep_i': [ + clihelp: 'Ignore case while using seqkit grep. ' + + "Defaut: " + (params.seqkit_grep_i ?: 'undefined'), + cliflag: '--seqkit_grep_i', + clivalue: (params.seqkit_grep_i ? ' ' : '') + ], + 'seqkit_grep_v': [ + clihelp: 'Invert the match i.e. select non-matching records. ' + + "Defaut: " + (params.seqkit_grep_v ?: 'undefined'), + cliflag: '--seqkit_grep_v', + clivalue: (params.seqkit_grep_v ? ' ' : '') + ], + 'seqkit_grep_m': [ + clihelp: 'Maximum mismatches when matching by sequence. ' + + "Defaut: " + (params.seqkit_grep_m ?: 'undefined'), + cliflag: '--seqkit_grep_m', + clivalue: (params.seqkit_grep_v ?: '') + ], + 'seqkit_grep_r': [ + clihelp: 'Input patters are regular expressions. ' + + "Defaut: " + (params.seqkit_grep_m ?: 'undefined'), + cliflag: '--seqkit_grep_m', + clivalue: (params.seqkit_grep_v ?: '') + ] + ] + + toolspecs.each { + k, v -> tool.text['--' + k] = "${v.clihelp}" + tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ] + } + + return tool +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/lib/help/seqkitrmdup.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,61 @@ +// Help text for seqkit rmdup within CPIPES. + +def seqkitrmdupHelp(params) { + +Map tool = [:] +Map toolspecs = [:] +tool.text = [:] +tool.helpparams = [:] + + toolspecs = [ + 'seqkit_rmdup_run': [ + clihelp: 'Remove duplicate sequences using seqkit rmdup. Default: ' + + (params.seqkit_rmdup_run ?: false), + cliflag: null, + clivalue: null + ], + 'seqkit_rmdup_n': [ + clihelp: 'Match and remove duplicate sequences by full name instead of just ID. ' + + "Defaut: ${params.seqkit_rmdup_n}", + cliflag: '-n', + clivalue: (params.seqkit_rmdup_n ? ' ' : '') + ], + 'seqkit_rmdup_s': [ + clihelp: 'Match and remove duplicate sequences by sequence content. ' + + "Defaut: ${params.seqkit_rmdup_s}", + cliflag: '-s', + clivalue: (params.seqkit_rmdup_s ? ' ' : '') + ], + 'seqkit_rmdup_d': [ + clihelp: 'Save the duplicated sequences to a file. ' + + "Defaut: ${params.seqkit_rmdup_d}", + cliflag: null, + clivalue: null + ], + 'seqkit_rmdup_D': [ + clihelp: 'Save the number and list of duplicated sequences to a file. ' + + "Defaut: ${params.seqkit_rmdup_D}", + cliflag: null, + clivalue: null + ], + 'seqkit_rmdup_i': [ + clihelp: 'Ignore case while using seqkit rmdup. ' + + "Defaut: ${params.seqkit_rmdup_i}", + cliflag: '-i', + clivalue: (params.seqkit_rmdup_i ? ' ' : '') + ], + 'seqkit_rmdup_P': [ + clihelp: "Only consider positive strand (i.e. 5') when comparing by sequence content. " + + "Defaut: ${params.seqkit_rmdup_P}", + cliflag: '-P', + clivalue: (params.seqkit_rmdup_P ? ' ' : '') + ] + ] + + toolspecs.each { + k, v -> tool.text['--' + k] = "${v.clihelp}" + tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ] + } + + return tool +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/lib/help/seqsero2.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,50 @@ +def seqsero2Help(params) { + + Map tool = [:] + Map toolspecs = [:] + tool.text = [:] + tool.helpparams = [:] + + toolspecs = [ + 'seqsero2_run': [ + clihelp: "Run SeqSero2 tool. Default: ${params.seqsero2_run}", + cliflag: null, + clivalue: null + ], + 'seqsero2_t': [ + clihelp: "'1' for interleaved paired-end reads, '2' for " + + "separated paired-end reads, '3' for single reads, '4' for " + + "genome assembly, '5' for nanopore reads (fasta/fastq). " + + "Default: ${params.seqsero2_t}", + cliflag: '-t', + clivalue: (params.seqsero2_t ?: '') + ], + 'seqsero2_m': [ + clihelp: "Which workflow to apply, 'a'(raw reads allele " + + "micro-assembly), 'k'(raw reads and genome assembly k-mer). " + + "Default: ${params.seqsero2_m}", + cliflag: '-m', + clivalue: (params.seqsero2_m ?: '') + ], + 'seqsero2_c': [ + clihelp: 'SeqSero2 will only output serotype prediction without the directory ' + + 'containing log files. ' + + "Default: ${params.seqsero2_c}", + cliflag: '-c', + clivalue: (params.seqsero2_c ? ' ' : '') + ], + 'seqsero2_s': [ + clihelp: 'SeqSero2 will not output header in SeqSero_result.tsv. ' + + "Default: ${params.seqsero2_s}", + cliflag: '-l', + clivalue: (params.seqsero2_s ? ' ' : '') + ] + ] + + toolspecs.each { + k, v -> tool.text['--' + k] = "${v.clihelp}" + tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ] + } + + return tool +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/lib/help/serotypefinder.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,46 @@ +def serotypefinderHelp(params) { + + Map tool = [:] + Map toolspecs = [:] + tool.text = [:] + tool.helpparams = [:] + + toolspecs = [ + 'serotypefinder_run': [ + clihelp: "Run SerotypeFinder tool. Default: ${params.serotypefinder_run}", + cliflag: null, + clivalue: null + ], + 'serotypefinder_x': [ + clihelp: 'Generate extended output files. ' + + "Default: ${params.serotypefinder_x}", + cliflag: '-x', + clivalue: (params.serotypefinder_x ? ' ' : '') + ], + 'serotypefinder_db': [ + clihelp: 'Path to SerotypeFinder databases. ' + + "Default: ${params.serotypefinder_db}", + cliflag: '-p', + clivalue: null + ], + 'serotypefinder_min_threshold': [ + clihelp: 'Minimum percent identity (in float) required for calling a hit. ' + + "Default: ${params.serotypefinder_min_threshold}", + cliflag: '-t', + clivalue: (params.serotypefinder_min_threshold ?: '') + ], + 'serotypefinder_min_cov': [ + clihelp: 'Minumum percent coverage (in float) required for calling a hit. ' + + "Default: ${params.serotypefinder_min_cov}", + cliflag: '-l', + clivalue: (params.serotypefinder_min_cov ?: '') + ] + ] + + toolspecs.each { + k, v -> tool.text['--' + k] = "${v.clihelp}" + tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ] + } + + return tool +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/lib/help/spades.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,121 @@ +// Help text for spades within CPIPES. + +def spadesHelp(params) { + +Map tool = [:] +Map toolspecs = [:] +tool.text = [:] +tool.helpparams = [:] + + toolspecs = [ + 'spades_run': [ + clihelp: 'Run SPAdes assembler. Default: ' + + (params.spades_run ?: false), + cliflag: null, + clivalue: null + ], + 'spades_isolate': [ + clihelp: 'This flag is highly recommended for high-coverage isolate and ' + + "multi-cell data. Defaut: ${params.spades_isolate}", + cliflag: '--isolate', + clivalue: (params.spades_isolate ? ' ' : '') + ], + 'spades_sc': [ + clihelp: 'This flag is required for MDA (single-cell) data. ' + + "Default: ${params.spades_sc}", + cliflag: '--sc', + clivalue: (params.spades_sc ? ' ' : '') + ], + 'spades_meta': [ + clihelp: 'This flag is required for metagenomic data. ' + + "Default: ${params.spades_meta}", + cliflag: '--meta', + clivalue: (params.spades_meta ? ' ' : '') + ], + 'spades_bio': [ + clihelp: 'This flag is required for biosytheticSPAdes mode. ' + + "Default: ${params.spades_bio}", + cliflag: '--bio', + clivalue: (params.spades_bio ? ' ' : '') + ], + 'spades_corona': [ + clihelp: 'This flag is required for coronaSPAdes mode. ' + + "Default: ${params.spades_corona}", + cliflag: '--corona', + clivalue: (params.spades_corona ? ' ' : '') + ], + 'spades_rna': [ + clihelp: 'This flag is required for RNA-Seq data. ' + + "Default: ${params.spades_rna}", + cliflag: '--rna', + clivalue: (params.spades_rna ? ' ' : '') + ], + 'spades_plasmid': [ + clihelp: 'Runs plasmidSPAdes pipeline for plasmid detection. ' + + "Default: ${params.spades_plasmid}", + cliflag: '--plasmid', + clivalue: (params.spades_plasmid ? ' ' : '') + ], + 'spades_metaviral': [ + clihelp: 'Runs metaviralSPAdes pipeline for virus detection. ' + + "Default: ${params.spades_metaviral}", + cliflag: '--metaviral', + clivalue: (params.spades_metaviral ? ' ' : '') + ], + 'spades_metaplasmid': [ + clihelp: 'Runs metaplasmidSPAdes pipeline for plasmid detection in ' + + "metagenomics datasets. Default: ${params.spades_metaplasmid}", + cliflag: '--metaplasmid', + clivalue: (params.spades_metaplasmid ? ' ' : '') + ], + 'spades_rnaviral': [ + clihelp: 'This flag enables virus assembly module from RNA-Seq data. ' + + "Default: ${params.spades_rnaviral}", + cliflag: '--rnaviral', + clivalue: (params.spades_rnaviral ? ' ' : '') + ], + 'spades_iontorrent': [ + clihelp: 'This flag is required for IonTorrent data. ' + + "Default: ${params.spades_iontorrent}", + cliflag: '--iontorrent', + clivalue: (params.spades_iontorrent ? ' ' : '') + ], + 'spades_only_assembler': [ + clihelp: 'Runs only the SPAdes assembler module (without read error correction). ' + + "Default: ${params.spades_only_assembler}", + cliflag: '--only-assembler', + clivalue: (params.spades_only_assembler ? ' ' : '') + ], + 'spades_careful': [ + clihelp: 'Tries to reduce the number of mismatches and short indels in the assembly. ' + + "Default: ${params.spades_careful}", + cliflag: '--careful', + clivalue: (params.spades_careful ? ' ' : '') + ], + 'spades_cov_cutoff': [ + clihelp: 'Coverage cutoff value (a positive float number). ' + + "Default: ${params.spades_cov_cutoff}", + cliflag: '--cov-cutoff', + clivalue: (params.spades_cov_cutoff ?: '') + ], + 'spades_k': [ + clihelp: 'List of k-mer sizes (must be odd and less than 128). ' + + "Default: ${params.spades_k}", + cliflag: '-k', + clivalue: (params.spades_k ?: '') + ], + 'spades_hmm': [ + clihelp: 'Directory with custom hmms that replace the default ones (very rare). ' + + "Default: ${params.spades_hmm}", + cliflag: '--custom-hmms', + clivalue: (params.spades_hmm ?: '') + ] + ] + + toolspecs.each { + k, v -> tool.text['--' + k] = "${v.clihelp}" + tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ] + } + + return tool +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/lib/routines.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,397 @@ +// Hold methods to print: +// 1. Colored logo. +// 2. Summary of parameters. +// 3. Single dashed line. +// 4. Double dashed line. +// + +import groovy.json.JsonSlurper +import groovy.util.ConfigSlurper +// import nextflow.config.ConfigParser +// import nextflow.config.ConfigBuilder +// import groovy.json.JsonOutput + +// ASCII logo +def pipelineBanner() { + + def padding = (params.pad) ?: 30 + Map fgcolors = getANSIColors() + + def banner = [ + name: "${fgcolors.magenta}${workflow.manifest.name}${fgcolors.reset}", + author: "${fgcolors.cyan}${workflow.manifest.author}${fgcolors.reset}", + // workflow: "${fgcolors.magenta}${params.pipeline}${fgcolors.reset}", + version: "${fgcolors.green}${workflow.manifest.version}${fgcolors.reset}", + center: "${fgcolors.green}${params.center}${fgcolors.reset}", + pad: padding + ] + + manifest = addPadding(banner) + + return """${fgcolors.white}${dashedLine(type: '=')}${fgcolors.magenta} + (o) + ___ _ __ _ _ __ ___ ___ + / __|| '_ \\ | || '_ \\ / _ \\/ __| +| (__ | |_) || || |_) || __/\\__ \\ + \\___|| .__/ |_|| .__/ \\___||___/ + | | | | + |_| |_|${fgcolors.reset} +${dashedLine()} +${fgcolors.blue}A collection of modular pipelines at CFSAN, FDA.${fgcolors.reset} +${dashedLine()} +${manifest} +${dashedLine(type: '=')} +""".stripIndent() +} + +// Add padding to keys so that +// they indent nicely on the +// terminal +def addPadding(values) { + + def pad = (params.pad) ?: 30 + values.pad = pad + + def padding = values.pad.toInteger() + def nocapitalize = values.nocapitalize + def stopnow = values.stopNow + def help = values.help + + values.removeAll { + k, v -> [ + 'nocapitalize', + 'pad', + 'stopNow', + 'help' + ].contains(k) + } + + values.keySet().each { k -> + v = values[k] + s = params.linewidth - (pad + 5) + if (v.toString().size() > s && !stopnow) { + def sen = '' + // v.toString().findAll(/.{1,${s}}\b(?:\W*|\s*)/).each { + // sen += ' '.multiply(padding + 2) + it + '\n' + // } + v.toString().eachMatch(/.{1,${s}}(?=.*)\b|\w+/) { + sen += ' '.multiply(padding + 2) + it.trim() + '\n' + } + values[k] = ( + help ? sen.replaceAll(/^(\n|\s)*/, '') : sen.trim() + ) + } else { + values[k] = (help ? v + "\n" : v) + } + k = k.replaceAll(/\./, '_') + } + + return values.findResults { + k, v -> nocapitalize ? + k.padRight(padding) + ': ' + v : + k.capitalize().padRight(padding) + ': ' + v + }.join("\n") +} + +// Method for error messages +def stopNow(msg) { + + Map fgcolors = getANSIColors() + Map errors = [:] + + if (msg == null) { + msg = "Unknown error" + } + + errors['stopNow'] = true + errors["${params.cfsanpipename} - ${params.pipeline} - ERROR"] = """ +${fgcolors.reset}${dashedLine()} +${fgcolors.red}${msg}${fgcolors.reset} +${dashedLine()} +""".stripIndent() + // println dashedLine() // defaults to stdout + // log.info addPadding(errors) // prints to stdout + exit 1, "\n" + dashedLine() + + "${fgcolors.red}\n" + addPadding(errors) +} + +// Method to validate 4 required parameters +// if input for entry point is FASTQ files +def validateParamsForFASTQ() { + switch (params) { + case { params.metadata == null && params.input == null }: + stopNow("Either metadata CSV file with 5 required columns\n" + + "in order: sample, fq1, fq2, strandedness, single_end or \n" + + "input directory of only FASTQ files (gzipped or unzipped) should be provided\n" + + "using --metadata or --input options.\n" + + "None of these two options were provided!") + break + case { params.metadata != null && params.input != null }: + stopNow("Either metadata or input directory of FASTQ files\n" + + "should be provided using --metadata or --input options.\n" + + "Using both these options is not allowed!") + break + case { params.output == null }: + stopNow("Please mention output directory to store all results " + + "using --output option!") + break + } + return 1 +} + +// Method to print summary of parameters +// before running +def summaryOfParams() { + + // def pipeline_specific_config = pipeline_specific_config = new ConfigParser().setIgnoreIncludes(true).parse( + // file("${params.workflowsconf}${params.fs}${params.pipeline}.config").text + // ) + def pipeline_specific_config = new ConfigSlurper().parse( + file("${params.workflowsconf}${params.fs}${params.pipeline}.config").text + ) + + Map fgcolors = getANSIColors() + Map globalparams = [:] + Map localparams = params.subMap( + pipeline_specific_config.params.keySet().toList() + params.logtheseparams + ) + + if (localparams !instanceof Map) { + stopNow("Need a Map of paramters. We got: " + localparams.getClass()) + } + + if (localparams.size() != 0) { + localparams['nocapitalize'] = true + globalparams['nocapitalize'] = true + globalparams['nextflow_version'] = "${nextflow.version}" + globalparams['nextflow_build'] = "${nextflow.build}" + globalparams['nextflow_timestamp'] = "${nextflow.timestamp}" + globalparams['workflow_projectDir'] = "${workflow.projectDir}" + globalparams['workflow_launchDir'] = "${workflow.launchDir}" + globalparams['workflow_workDir'] = "${workflow.workDir}" + globalparams['workflow_container'] = "${workflow.container}" + globalparams['workflow_containerEngine'] = "${workflow.containerEngine}" + globalparams['workflow_runName'] = "${workflow.runName}" + globalparams['workflow_sessionId'] = "${workflow.sessionId}" + globalparams['workflow_profile'] = "${workflow.profile}" + globalparams['workflow_start'] = "${workflow.start}" + globalparams['workflow_commandLine'] = "${workflow.commandLine}" + return """${dashedLine()} +Summary of the current workflow (${fgcolors.magenta}${params.pipeline}${fgcolors.reset}) parameters +${dashedLine()} +${addPadding(localparams)} +${dashedLine()} +${fgcolors.cyan}N E X T F L O W${fgcolors.reset} - ${fgcolors.magenta}${params.cfsanpipename}${fgcolors.reset} - Runtime metadata +${dashedLine()} +${addPadding(globalparams)} +${dashedLine()}""".stripIndent() + } + return 1 +} + +// Method to display +// Return dashed line either '-' +// type or '=' type +def dashedLine(Map defaults = [:]) { + + Map fgcolors = getANSIColors() + def line = [color: 'white', type: '-'] + + if (!defaults.isEmpty()) { + line.putAll(defaults) + } + + return fgcolors."${line.color}" + + "${line.type}".multiply(params.linewidth) + + fgcolors.reset +} + +// Return slurped keys parsed from JSON +def slurpJson(file) { + def slurped = null + def jsonInst = new JsonSlurper() + + try { + slurped = jsonInst.parse(new File ("${file}")) + } + catch (Exception e) { + log.error 'Please check your JSON schema. Invalid JSON file: ' + file + } + + // Declare globals for the nanofactory + // workflow. + return [keys: slurped.keySet().toList(), cparams: slurped] +} + +// Default help text in a map if the entry point +// to a pipeline is FASTQ files. +def fastqEntryPointHelp() { + + Map helptext = [:] + Map fgcolors = getANSIColors() + + helptext['Workflow'] = "${fgcolors.magenta}${params.pipeline}${fgcolors.reset}" + helptext['Author'] = "${fgcolors.cyan}${params.workflow_built_by}${fgcolors.reset}" + helptext['Version'] = "${fgcolors.green}${params.workflow_version}${fgcolors.reset}\n" + helptext['Usage'] = "cpipes --pipeline ${params.pipeline} [options]\n" + helptext['Required'] = "" + helptext['--input'] = "Absolute path to directory containing FASTQ files. " + + "The directory should contain only FASTQ files as all the " + + "files within the mentioned directory will be read. " + + "Ex: --input /path/to/fastq_pass" + helptext['--output'] = "Absolute path to directory where all the pipeline " + + "outputs should be stored. Ex: --output /path/to/output" + helptext['Other options'] = "" + helptext['--metadata'] = "Absolute path to metadata CSV file containing five " + + "mandatory columns: sample,fq1,fq2,strandedness,single_end. The fq1 and fq2 " + + "columns contain absolute paths to the FASTQ files. This option can be used in place " + + "of --input option. This is rare. Ex: --metadata samplesheet.csv" + helptext['--fq_suffix'] = "The suffix of FASTQ files (Unpaired reads or R1 reads or Long reads) if " + + "an input directory is mentioned via --input option. Default: ${params.fq_suffix}" + helptext['--fq2_suffix'] = "The suffix of FASTQ files (Paired-end reads or R2 reads) if an input directory is mentioned via " + + "--input option. Default: ${params.fq2_suffix}" + helptext['--fq_filter_by_len'] = "Remove FASTQ reads that are less than this many bases. " + + "Default: ${params.fq_filter_by_len}" + helptext['--fq_strandedness'] = "The strandedness of the sequencing run. This is mostly needed " + + "if your sequencing run is RNA-SEQ. For most of the other runs, it is probably safe to use " + + "unstranded for the option. Default: ${params.fq_strandedness}" + helptext['--fq_single_end'] = "SINGLE-END information will be auto-detected but this option forces " + + "PAIRED-END FASTQ files to be treated as SINGLE-END so only read 1 information is included in " + + "auto-generated samplesheet. Default: ${params.fq_single_end}" + helptext['--fq_filename_delim'] = "Delimiter by which the file name is split to obtain sample name. " + + "Default: ${params.fq_filename_delim}" + helptext['--fq_filename_delim_idx'] = "After splitting FASTQ file name by using the --fq_filename_delim option," + + " all elements before this index (1-based) will be joined to create final sample name." + + " Default: ${params.fq_filename_delim_idx}" + + return helptext +} + +// Show concise help text if configured within the main workflow. +def conciseHelp(def tool = null) { + Map fgcolors = getANSIColors() + + tool ?= "fastp" + tools = tool?.tokenize(',') + + return """ +${dashedLine()} +Show configurable CLI options for each tool within ${fgcolors.magenta}${params.pipeline}${fgcolors.reset} +${dashedLine()} +Ex: cpipes --pipeline ${params.pipeline} --help +""" + (tools.size() > 1 ? "Ex: cpipes --pipeline ${params.pipeline} --help ${tools[0]}" + + """ +Ex: cpipes --pipeline ${params.pipeline} --help ${tools[0]},${tools[1]} +${dashedLine()}""".stripIndent() : """Ex: cpipes --pipeline ${params.pipeline} --help ${tool} +${dashedLine()}""".stripIndent()) + +} + +// Wrap help text with the following options +def wrapUpHelp() { + + return [ + 'Help options' : "", + '--help': "Display this message.\n", + 'help': true, + 'nocapitalize': true + ] +} + +// Method to send email on workflow complete. +def sendMail() { + + if (params.user_email == null) { + return 1 + } + + def pad = (params.pad) ?: 30 + def contact_emails = [ + stakeholder: (params.workflow_blueprint_by ?: 'Not defined'), + author: (params.workflow_built_by ?: 'Not defined') + ] + def msg = """ +${pipelineBanner()} +${summaryOfParams()} +${params.cfsanpipename} - ${params.pipeline} +${dashedLine()} +Please check the following directory for N E X T F L O W +reports. You can view the HTML files directly by double clicking +them on your workstation. +${dashedLine()} +${params.tracereportsdir} +${dashedLine()} +Please send any bug reports to CFSAN Dev Team or the author or +the stakeholder of the current pipeline. +${dashedLine()} +Error messages (if any) +${dashedLine()} +${workflow.errorMessage} +${workflow.errorReport} +${dashedLine()} +Contact emails +${dashedLine()} +${addPadding(contact_emails)} +${dashedLine()} +Thank you for using ${params.cfsanpipename} - ${params.pipeline}! +${dashedLine()} +""".stripIndent() + + def mail_cmd = [ + 'sendmail', + '-f', 'noreply@gmail.com', + '-F', 'noreply', + '-t', "${params.user_email}" + ] + + def email_subject = "${params.cfsanpipename} - ${params.pipeline}" + Map fgcolors = getANSIColors() + + if (workflow.success) { + email_subject += ' completed successfully!' + } + else if (!workflow.success) { + email_subject += ' has failed!' + } + + try { + ['env', 'bash'].execute() << """${mail_cmd.join(' ')} +Subject: ${email_subject} +Mime-Version: 1.0 +Content-Type: text/html +<pre> +${msg.replaceAll(/\x1b\[[0-9;]*m/, '')} +</pre> +""".stripIndent() + } catch (all) { + def warning_msg = "${fgcolors.yellow}${params.cfsanpipename} - ${params.pipeline} - WARNING" + .padRight(pad) + ':' + log.info """ +${dashedLine()} +${warning_msg} +${dashedLine()} +Could not send mail with the sendmail command! +${dashedLine()} +""".stripIndent() + } + return 1 +} + +// Set ANSI colors for any and all +// STDOUT or STDERR +def getANSIColors() { + + Map fgcolors = [:] + + fgcolors['reset'] = "\033[0m" + fgcolors['black'] = "\033[0;30m" + fgcolors['red'] = "\033[0;31m" + fgcolors['green'] = "\033[0;32m" + fgcolors['yellow'] = "\033[0;33m" + fgcolors['blue'] = "\033[0;34m" + fgcolors['magenta'] = "\033[0;35m" + fgcolors['cyan'] = "\033[0;36m" + fgcolors['white'] = "\033[0;37m" + + return fgcolors +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/abricate/run/README.md Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,94 @@ +# NextFlow DSL2 Module + +```bash +ABRICATE_RUN +``` + +## Description + +Run `abricate` tool on a list of assembled contigs in FASTA format given a list of database names. Produces a single output table in ASCII text format per database. + +\ + + +### `input:` + +___ + +Type: `tuple` + +Takes in the following tuple of metadata (`meta`) and a list of assemled contig FASTA files of input type `path` (`assembly`). + +Ex: + +```groovy +[ [id: 'sample1', single_end: true], '/data/sample1/f_assembly.fa' ] +``` + +\ + + +#### `meta` + +Type: Groovy Map + +A Groovy Map containing the metadata about the FASTQ file. + +Ex: + +```groovy +[ id: 'FAL00870', strandedness: 'unstranded', single_end: true ] +``` + +\ + + +#### `assembly` + +Type: `path` + +NextFlow input type of `path` pointing to assembled contig file in FASTA format. + +\ + + +#### `abdbs` + +Type: `val` + +Nextflow input type of `val` containing a list of at least one of the following database names on which `abricate` should be run. + +Ex: + +```groovy +[ 'resfinder', 'megares', 'ncbi', 'ncbiamrplus', 'argannot' , 'ecoli_vf' ] +``` + +\ + + +### `output:` + +___ + +Type: `tuple` + +Outputs a tuple of metadata (`meta` from `input:`) and list of `abricate` result files (`abricated`). + +\ + + +#### `abricated` + +Type: `path` + +NextFlow output type of `path` pointing to the `abricate` results table file per sample (`id:`). + +\ + + +#### `versions` + +Type: `path` + +NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/abricate/run/main.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,48 @@ +process ABRICATE_RUN { + tag "$meta.id" + label 'process_low' + + module (params.enable_module ? "${params.swmodulepath}${params.fs}abricate${params.fs}1.0.1" : null) + conda (params.enable_conda ? "bioconda::abricate=1.0.1" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/abricate%3A1.0.1--ha8f3691_1': + 'quay.io/biocontainers/abricate:1.0.1--ha8f3691_1' }" + + input: + tuple val(meta), path(assembly) + val abdbs + + output: + path "${meta.id}${params.fs}*" + tuple val(meta), path("${meta.id}${params.fs}*.ab.txt"), emit: abricated + path "versions.yml" , emit: versions + + when: + (task.ext.when == null || task.ext.when) && assembly.size() > 0 + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def dbs = abdbs.collect().join('\\n') + """ + newprefix="${prefix}${params.fs}${prefix}" + + if [ ! -d "$prefix" ]; then + mkdir "$prefix" || exit 1 + fi + + echo -e "$dbs" | while read -r db; do + abricate \\ + $assembly \\ + $args \\ + --db \$db \\ + --threads $task.cpus 1> "\${newprefix}.\${db}.ab.txt" + done + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + abricate: \$(echo \$(abricate --version 2>&1) | sed 's/^.*abricate //' ) + bash: \$( bash --version 2>&1 | sed '1!d; s/^.*version //; s/ (.*\$//' ) + END_VERSIONS + """ +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/abricate/summary/README.md Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,140 @@ +# NextFlow DSL2 Module + +```bash +ABRICATE_SUMMARY +``` + +## Description + +Run `abricate` tool's `summary` sub-command on a list of `abricate`'s result table files per database. + +\ + + +### `input:` + +___ + +Type: `tuple` + +Takes in the following tuple of `abricate` database names of type `val` (`abdbs`) and a list of `abricate` result table files for all databases of type `path` (`abfiles`). + +Ex: + +```groovy +[ + [ 'megares', 'argannot', 'resfinder', 'ncbi' ], + [ '/data/sample1/f.ncbi.ab.txt', + '/data/sample1/f.megares.ab.txt', + '/data/sample1/f.resfinder.ab.txt', + '/data/sample1/f.argannot.ab.txt', + '/data/sample1/f2.ncbi.ab.txt', + '/data/sample1/f2.megares.ab.txt', + '/data/sample1/f2.resfinder.ab.txt', + '/data/sample1/f2.argannot.ab.txt' + ] +] +``` + +\ + + +#### `abdbs` + +Type: `val` + +A Groovy List containing the **mandatory** list of at least the following 4 `abricate` database names on which `abricate` was run. + +Ex: + +```groovy +[ 'resfinder', 'megares', 'ncbi', 'argannot' ] +``` + +\ + + +#### `abfiles` + +Type: `path` + +NextFlow input type of `path` pointing to `abricate` result files for each of the database. + +\ + + +### `output:` + +___ + +#### `ncbi` + +Type: `tuple` +\ +Optional: `true` + +Outputs a tuple of `abricate` database key (`abricate_ncbi`) and summary result file from `abricate summary` command of type `path` (`ncbi`). This database includes only core AMR genes. This tuple is emitted optionally only where there are output files with suffix `.ncbi.absum.txt` + +\ + + +#### `ncbiamrplus` + +Type: `tuple` +\ +Optional: `true` + +Outputs a tuple of `abricate` database key (`abricate_ncbiamrplus`) and summary result file from `abricate summary` command of type `path` (`ncbiamrplus`). This database includes both core AMR genes and plus AMR genes. This tuple is emitted optionally only where there are output files with suffix `.ncbiamrplus.absum.txt` + +\ + + +#### `resfinder` + +Type: `tuple` +\ +Optional: `true` + +Outputs a tuple of `abricate` database key (`abricate_resfinder`) and summary result file from `abricate summary` command of type `path` (`resfinder`). This tuple is emitted optionally only where there are output files with suffix `.resfinder.absum.txt` + +\ + + +#### `megares` + +Type: `tuple` +\ +Optional: `true` + +Outputs a tuple of `abricate` database key (`abricate_megares`) and summary result file from `abricate summary` command of type `path` (`megares`). This tuple is emitted optionally only where there are output files with suffix `.megares.absum.txt` + +\ + + +#### `argannot` + +Type: `tuple` +\ +Optional: `true` + +Outputs a tuple of `abricate` database key (`abricate_argannot`) and summary result file from `abricate summary` command of type `path` (`argannot`). This tuple is emitted optionally only where there are output files with suffix `.argannot.absum.txt` + +\ + + +#### `ecoli_vf` + +Type: `tuple` +\ +Optional: `true` + +Outputs an **optional** tuple of `abricate` database key (`abricate_ecoli_vf`) and summary result file from `abricate summary` command of type `path` (`ecoli_vf`). This tuple is emitted only when there are output files with suffix `.ecoli_vf.absum.txt` within the `work` folder. + +\ + + +#### `versions` + +Type: `path` + +NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/abricate/summary/main.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,80 @@ +process ABRICATE_SUMMARY { + tag "${abdbs.join(',')}" + label 'process_low' + + module (params.enable_module ? "${params.swmodulepath}${params.fs}abricate${params.fs}1.0.1" : null) + conda (params.enable_conda ? "bioconda::abricate=1.0.1 conda-forge::coreutils" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/abricate%3A1.0.1--ha8f3691_1': + 'quay.io/biocontainers/abricate:1.0.1--ha8f3691_1' }" + + input: + tuple val(abdbs), path(abfiles) + + output: + tuple val('abricate_ncbi'), path("*.ncbi.absum.txt") , emit: ncbi, optional: true + tuple val('abricate_ncbiamrplus'), path("*.ncbiamrplus.absum.txt"), emit: ncbiamrplus, optional: true + tuple val('abricate_resfinder'), path("*resfinder.absum.txt") , emit: resfinder, optional: true + tuple val('abricate_megares'), path("*.megares.absum.txt") , emit: megares, optional: true + tuple val('abricate_argannot'), path("*.argannot.absum.txt") , emit: argannot, optional: true + tuple val('abricate_ecoli_vf'), path("*.ecoli_vf.absum.txt") , emit: ecoli_vf, optional: true + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def onthese = abdbs.collect{ db -> + abfiles.findAll { files -> + files =~ /\.${db}/ + }.join(' ') + }.join('\\n') + """ + filenum="1" + + echo -e "$onthese" | while read -r files; do + db=\$( echo -e "\${files}" | grep -E -o '\\w+\\.ab\\.txt' | sort -u | sed -e 's/.ab.txt//' ) + + if [ -z "\$db" ]; then + db="\$filenum" + fi + + abricate \\ + $args \\ + --summary \${files} \\ + 1> "abricate.\${db}.absum.txt" + + sed -i -e "s/.\${db}.ab.txt//" "abricate.\${db}.absum.txt" + sed -i -e 's/.assembly_filtered_contigs.fasta//' "abricate.\${db}.absum.txt" + + filenum=\$((filenum+1)) + done + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + abricate: \$(echo \$(abricate --version 2>&1) | sed 's/^.*abricate //' ) + bash: \$( bash --version 2>&1 | sed '1!d; s/^.*version //; s/ (.*\$//' ) + END_VERSIONS + + sedver="" + sortver="" + grepver="" + + if [ "${workflow.containerEngine}" != "null" ]; then + sortver=\$( sort --help 2>&1 | sed -e '1!d; s/ (.*\$//' ) + sedver="\$sortver" + grepver="\$sortver" + else + sortver=\$( sort --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' ) + sedver=\$( echo \$(sed --version 2>&1) | sed 's/^.*(GNU sed) //; s/ Copyright.*\$//' ) + grepver=\$( echo \$(grep --version 2>&1) | sed 's/^.*(GNU grep) //; s/ Copyright.*\$//' ) + fi + + cat <<-END_VERSIONS >> versions.yml + sort: \$sortver + grep: \$grepver + sed: \$sedver + END_VERSIONS + """ +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/amrfinderplus/run/README.md Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,104 @@ +# NextFlow DSL2 Module + +```bash +AMRFINDERPLUS_RUN +``` + +## Description + +Run `amrfinder` tool on a list of assembled contigs in FASTA format. Produces a single output table in ASCII text format per database. + +\ + + +### `input:` + +___ + +Type: `tuple` + +Takes in the following tuple of metadata (`meta`) and a list of assemled contig FASTA file of input type `path` (`fasta`). + +Ex: + +```groovy +[ [id: 'sample1', single_end: true], '/data/sample1/f_assembly.fa' ] +``` + +\ + + +#### `meta` + +Type: Groovy Map + +A Groovy Map containing the metadata about the FASTQ file. + +Ex: + +```groovy +[ id: 'FAL00870', strandedness: 'unstranded', single_end: true, organism: 'Escherichia' ] +``` + +\ + + +#### `fasta` + +Type: `path` + +NextFlow input type of `path` pointing to assembled contig file in FASTA format. + +\ + + +#### `args` + +Type: Groovy String + +String of optional command-line arguments to be passed to the tool. This can be mentioned in `process` scope within `withName:process_name` block using `ext.args` option within your `nextflow.config` file. + +Ex: + +```groovy +withName: 'AMRFINDERPLUS_RUN' { + ext.args = '--gpipe_org' +} +``` + +### `output:` + +___ + +Type: `tuple` + +Outputs a tuple of metadata (`meta` from `input:`) and list of `amrfinder` result files (`report`). + +\ + + +#### `report` + +Type: `path` + +NextFlow output type of `path` pointing to the `amrfinder` results table file (`.tsv`) per sample (`id:`). + +\ + + +#### `mutional_report` + +Type: `path` +\ +Optional: `true` + +NextFlow output type of `path` pointing to the `amrfinder` mutation results table file (`.tsv`) per sample (`id:`). Obtaining this output will depend on the presence of the `organism` key in the metadata (`meta`). See example above. + +\ + + +#### `versions` + +Type: `path` + +NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/amrfinderplus/run/main.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,52 @@ +process AMRFINDERPLUS_RUN { + tag "$meta.id" + label 'process_low' + + module (params.enable_module ? "${params.swmodulepath}${params.fs}amrfinderplus${params.fs}3.10.24" : null) + conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.24 conda-forge::libgcc-ng" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus%3A3.10.23--h17dc2d4_0': + 'quay.io/biocontainers/ncbi-amrfinderplus:3.10.23--h17dc2d4_0' }" + + input: + tuple val(meta), path(fasta) + + output: + tuple val(meta), path("${prefix}.tsv") , emit: report + tuple val(meta), path("${prefix}-mutations.tsv"), emit: mutation_report, optional: true + path "versions.yml" , emit: versions + + when: + (task.ext.when == null || task.ext.when) && fasta.size() > 0 + + script: + def args = task.ext.args ?: '' + def is_compressed = fasta.getName().endsWith(".gz") ? true : false + prefix = task.ext.prefix ?: "${meta.id}" + organism_param = meta.containsKey("organism") ? "--organism ${meta.organism} --mutation_all ${prefix}-mutations.tsv" : "" + fasta_name = fasta.getName().replace(".gz", "") + fasta_param = "-n" + if (meta.containsKey("is_proteins")) { + if (meta.is_proteins) { + fasta_param = "-p" + } + } + """ + if [ "$is_compressed" == "true" ]; then + gzip -c -d $fasta > $fasta_name + fi + + amrfinder \\ + $fasta_param $fasta_name \\ + $organism_param \\ + $args \\ + --threads $task.cpus > ${prefix}.tsv + + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + amrfinderplus: \$(amrfinder --version) + gzip: \$( echo \$(gzip --version 2>&1) | sed 's/^.*(gzip) //; s/gzip //; s/ Copyright.*\$//' ) + END_VERSIONS + """ +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/cat/fastq/README.md Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,96 @@ +# NextFlow DSL2 Module + +```bash +CAT_FASTQ +``` + +## Description + +Concatenates a list of FASTQ files. Produces 2 files per sample (`id:`) if `single_end` is `false` as mentioned in the metadata Groovy Map. + +\ + + +### `input:` + +___ + +Type: `tuple` + +Takes in the following tuple of metadata (`meta`) and a list of FASTQ files of input type `path` (`reads`) to be concatenated. + +Ex: + +```groovy +[ [id: 'sample1', single_end: true], ['/data/sample1/f_L001.fq', '/data/sample1/f_L002.fq'] ] +``` + +\ + + +#### `meta` + +Type: Groovy Map + +A Groovy Map containing the metadata about the FASTQ file. + +Ex: + +```groovy +[ id: 'FAL00870', strandedness: 'unstranded', single_end: true ] +``` + +\ + + +#### `reads` + +Type: `path` + +NextFlow input type of `path` pointing to list of FASTQ files. + +\ + + +#### `args` + +Type: Groovy String + +String of optional command-line arguments to be passed to the tool. This can be mentioned in `process` scope within `withName:process_name` block using `ext.args` option within your `nextflow.config` file. + +Ex: + +```groovy +withName: 'CAT_FASTQ' { + ext.args = '--genome_size 5.5m' +} +``` + +\ + + +### `output:` + +___ + +Type: `tuple` + +Outputs a tuple of metadata (`meta` from `input:`) and list of concatenated FASTQ files (`catted_reads`). + +\ + + +#### `catted_reads` + +Type: `path` + +NextFlow output type of `path` pointing to the concatenated FASTQ files per sample (`id:`). + +\ + + +#### `versions` + +Type: `path` + +NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/cat/fastq/main.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,89 @@ +process CAT_FASTQ { + tag "$meta.id" + label 'process_micro' + + conda (params.enable_conda ? "conda-forge::sed=4.7 conda-forge::gzip" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' : + 'biocontainers/biocontainers:v1.2.0_cv1' }" + + input: + tuple val(meta), path(reads, stageAs: "input*/*") + + output: + tuple val(meta), path("*.merged.fastq.gz"), emit: catted_reads + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def readList = reads.collect{ it.toString() } + def is_in_gz = readList[0].endsWith('.gz') + def gz_or_ungz = (is_in_gz ? '' : ' | gzip') + def pigz_or_ungz = (is_in_gz ? '' : " | pigz -p ${task.cpus}") + if (meta.single_end) { + if (readList.size > 1) { + """ + zcmd="gzip" + zver="" + + if type pigz > /dev/null 2>&1; then + cat ${readList.join(' ')} ${pigz_or_ungz} > ${prefix}.merged.fastq.gz + zcmd="pigz" + zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed -e '1!d' | sed "s/\$zcmd //" ) + else + cat ${readList.join(' ')} ${gz_or_ungz} > ${prefix}.merged.fastq.gz + zcmd="gzip" + + if [ "${workflow.containerEngine}" != "null" ]; then + zver=\$( echo \$( \$zcmd --help 2>&1 ) | sed -e '1!d; s/ (.*\$//' ) + else + zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed "s/^.*(\$zcmd) //; s/\$zcmd //; s/ Copyright.*\$//" ) + fi + fi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + cat: \$( echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//' ) + \$zcmd: \$zver + END_VERSIONS + """ + } + } else { + if (readList.size > 2) { + def read1 = [] + def read2 = [] + readList.eachWithIndex{ v, ix -> ( ix & 1 ? read2 : read1 ) << v } + """ + zcmd="gzip" + zver="" + + if type pigz > /dev/null 2>&1; then + cat ${read1.join(' ')} ${pigz_or_ungz} > ${prefix}_1.merged.fastq.gz + cat ${read2.join(' ')} ${pigz_or_ungz} > ${prefix}_2.merged.fastq.gz + zcmd="pigz" + zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed -e '1!d' | sed "s/\$zcmd //" ) + else + cat ${read1.join(' ')} ${gz_or_ungz} > ${prefix}_1.merged.fastq.gz + cat ${read2.join(' ')} ${gz_or_ungz} > ${prefix}_2.merged.fastq.gz + zcmd="gzip" + + if [ "${workflow.containerEngine}" != "null" ]; then + zver=\$( echo \$( \$zcmd --help 2>&1 ) | sed -e '1!d; s/ (.*\$//' ) + else + zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed "s/^.*(\$zcmd) //; s/\$zcmd //; s/ Copyright.*\$//" ) + fi + fi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + cat: \$( echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//' ) + \$zcmd: \$zver + END_VERSIONS + """ + } + } +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/cat/tables/README.md Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,88 @@ +# NextFlow DSL2 Module + +```bash +TABLE_SUMMARY +``` + +## Description + +Concatenates a list of tables (CSV or TAB delimited) in `.txt` or `.csv` format. The table files to be concatenated **must** have a header as the header from one of the table files will be used as the header for the concatenated result table file. + +\ + + +### `input:` + +___ + +Type: `tuple` + +Takes in the following tuple of `val` table key (`table_sum_on`) and a list of table files of input type `path` (`tables`) to be concatenated. For this module to work, a `bin` directory with the script `create_mqc_data_table.py` should be present where the NextFlow script using this DSL2 module will be run. This `python` script will convert the aggregated table to `.yml` format to be used with `multiqc`. + +Ex: + +```groovy +[ ['ectyper'], ['/data/sample1/f1_ectyper.txt', '/data/sample2/f2_ectyper.txt'] ] +``` + +\ + + +#### `table_sum_on` + +Type: `val` + +A single key defining what tables are being concatenated. For example, if all the `ectyper` results are being concatenated for all samples, then this can be `ectyper`. + +Ex: + +```groovy +[ ['ectyper'], ['/data/sample1/f1_ectyper.txt', '/data/sample2/f2_ectyper.txt'] ] +``` + +\ + + +#### `tables` + +Type: `path` + +NextFlow input type of `path` pointing to a list of tables (files) to be concatenated. + +\ + + +### `output:` + +___ + +Type: `tuple` + +Outputs a tuple of table key (`table_sum_on` from `input:`) and list of concatenated table files (`tblsummed`). + +\ + + +#### `tblsummed` + +Type: `path` + +NextFlow output type of `path` pointing to the concatenated table files per table key (Ex: `ectyper`). + +\ + + +#### `mqc_yml` + +Type: `path` + +NextFlow output type of `path` pointing to the `.yml` file storing table contents in `YAML` format which can be used to inject this table as part of the `multiqc` report. + +\ + + +#### `versions` + +Type: `path` + +NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/cat/tables/main.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,58 @@ +process TABLE_SUMMARY { + tag "$table_sum_on" + label 'process_low' + + // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container + module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null) + conda (params.enable_conda ? "conda-forge::python=3.9 conda-forge::pyyaml conda-forge::coreutils" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0' : + 'quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0' }" + + input: + tuple val(table_sum_on), path(tables) + + output: + tuple val(table_sum_on), path("*.tblsum.txt"), emit: tblsummed + path "*_mqc.yml" , emit: mqc_yml + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when || tables + + script: + def args = task.ext.args ?: '' + def onthese = tables.collect().join('\\n') + """ + filenum="1" + header="" + + echo -e "$onthese" | while read -r file; do + + if [ "\${filenum}" == "1" ]; then + header=\$( head -n1 "\${file}" ) + echo -e "\${header}" > ${table_sum_on}.tblsum.txt + fi + + tail -n+2 "\${file}" >> ${table_sum_on}.tblsum.txt + + filenum=\$((filenum+1)) + done + + create_mqc_data_table.py $table_sum_on ${workflow.manifest.name} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bash: \$( bash --version 2>&1 | sed '1!d; s/^.*version //; s/ (.*\$//' ) + python: \$( python --version | sed 's/Python //g' ) + END_VERSIONS + + headver=\$( head --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' ) + tailver=\$( tail --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' ) + + cat <<-END_VERSIONS >> versions.yml + head: \$headver + tail: \$tailver + END_VERSIONS + """ +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/centrifuge/classify/README.md Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,159 @@ +# NextFlow DSL2 Module + +```bash +CENTRIFUGE_CLASSIFY +``` + +## Description + +Run `centrifuge` tool on reads in FASTQ format. Produces 3 output files in ASCII text format and optional output files. + +\ + + +### `input:` + +___ + +Type: `tuple` + +Takes in the following tuple of metadata (`meta`) and a list of reads of type `path` (`reads`) per sample (`id:`). + +Ex: + +```groovy +[ + [ id: 'FAL00870', + strandedness: 'unstranded', + single_end: true, + centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab' + ], + '/hpc/scratch/test/FAL000870/f1.merged.fq.gz' +] +``` + +\ + + +#### `meta` + +Type: Groovy Map + +A Groovy Map containing the metadata about the FASTQ file. + +Ex: + +```groovy +[ + id: 'FAL00870', + strandedness: 'unstranded', + single_end: true, + centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab' +] +``` + +\ + + +#### `reads` + +Type: `path` + +NextFlow input type of `path` pointing to FASTQ files on which `centrifuge` classification should be run. + +\ + + +#### `args` + +Type: Groovy String + +String of optional command-line arguments to be passed to the tool. This can be mentioned in `process` scope within `withName:process_name` block using `ext.args` option within your `nextflow.config` file. + +Ex: + +```groovy +withName: 'CENTRIFUGE_CLASSIFY' { + ext.args = '--met 3' +} +``` + +\ + + +### `output:` + +___ + +Type: `tuple` + +Outputs a tuple of metadata (`meta` from `input:`) and list of `centrifuge` result files. + +\ + + +#### `report` + +Type: `path` + +NextFlow output type of `path` pointing to the `centrifuge` report table file (`.report.txt`) per sample (`id:`). + +\ + + +#### `output` + +Type: `path` + +NextFlow output type of `path` pointing to the `centrifuge` output table file (`.output.txt`) per sample (`id:`). + +\ + + +#### `kreport` + +Type: `path` + +NextFlow output type of `path` pointing to the `centrifuge` **Kraken** style report table file (`.kreport.txt`) per sample (`id:`). + +\ + + +#### `sam` + +Type: `path` +\ +Optional: `true` + +NextFlow output type of `path` pointing to the `centrifuge` alignment results in SAM (`.sam`) format per sample (`id:`). Obtaining this output will depend on the mention of `--centrifuge_out_fmt_sam` command-line option when the NextFlow pipeline is called. + +\ + + +#### `fastq_mapped` + +Type: `path` +\ +Optional: `true` + +NextFlow output type of `path` pointing to the `centrifuge` alignment results in FASTQ (`.fastq.gz`) format per sample (`id:`). Obtaining this output will depend on the mention of `--centrifuge_save_aligned` command-line option when the NextFlow pipeline is called. + +\ + + +#### `fastq_unmapped` + +Type: `path` +\ +Optional: `true` + +NextFlow output type of `path` pointing to the `centrifuge` FASTQ (`.fastq.gz`) files of unaligned reads per sample (`id:`). Obtaining this output will depend on the mention of `--centrifuge_save_unaligned` command-line option when the NextFlow pipeline is called. + +\ + + +#### `versions` + +Type: `path` + +NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/centrifuge/classify/main.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,61 @@ +process CENTRIFUGE_CLASSIFY { + tag "$meta.id" + label 'process_medium' + + module (params.enable_module ? 'centrifuge' : null) + conda (params.enable_conda ? "bioconda::centrifuge=1.0.4_beta" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4_beta--h9a82719_6' : + 'quay.io/biocontainers/centrifuge:1.0.4_beta--h9a82719_6' }" + + input: + tuple val(meta), path(reads) + + output: + tuple val(meta), path('*.report.txt') , emit: report + tuple val(meta), path('*.output.txt') , emit: output + tuple val(meta), path('*.kreport.txt') , emit: kreport + tuple val(meta), path('*.sam') , optional: true, emit: sam + tuple val(meta), path('*.mapped.fastq{,.1,.2}.gz') , optional: true, emit: fastq_mapped + tuple val(meta), path('*.unmapped.fastq{,.1,.2}.gz') , optional: true, emit: fastq_unmapped + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def paired = meta.single_end ? "-U ${reads}" : "-1 ${reads[0]} -2 ${reads[1]}" + def db = meta.centrifuge_x ?: '' + def db_name = db.toString().replace(".tar.gz","") + def unaligned = '' + def aligned = '' + if (meta.single_end) { + unaligned = params.centrifuge_save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : '' + aligned = params.centrifuge_save_aligned ? "--al-gz ${prefix}.mapped.fastq.gz" : '' + } else { + unaligned = params.centrifuge_save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : '' + aligned = params.centrifuge_save_aligned ? "--al-conc-gz ${prefix}.mapped.fastq.gz" : '' + } + def sam_output = params.centrifuge_out_fmt_sam ? "--out-fmt 'sam'" : '' + """ + centrifuge \\ + -x $db \\ + -p $task.cpus \\ + $paired \\ + --report-file ${prefix}.centrifuge.report.txt \\ + -S ${prefix}.centrifuge.output.txt \\ + $unaligned \\ + $aligned \\ + $sam_output \\ + $args + + centrifuge-kreport -x $db_name ${prefix}.centrifuge.output.txt > ${prefix}.centrifuge.kreport.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + centrifuge: \$( centrifuge --version | sed -n 1p | sed 's/^.*centrifuge-class version //') + END_VERSIONS + """ +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/centrifuge/extract/README.md Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,113 @@ +# NextFlow DSL2 Module + +```bash +CENTRIFUGE_EXTRACT +``` + +## Description + +Extract FASTQ reads given a FASTQ file originally used with `centrifuge` tool and a taxa of interest. This specific module uses only GNU Coreutils to create a list of FASTQ read ids that need to be extract. See also `CENTRIFUGE_PROCESS` module which uses a `python` script to generate the FASTQ read ids. + +\ + + +### `input:` + +___ + +Type: `tuple` + +Takes in the following 2 tuples: + +- A tuple of metadata (`meta`) and of type `path` (`centrifuge_output`) per sample (`id:`). + +- A tuple of metadata (`meta`) and of type `path` (`centrifuge_report`) per sample (`id:`). + +Ex: + +```groovy +[ + [ id: 'FAL00870', + strandedness: 'unstranded', + single_end: true, + centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab' + ], + '/hpc/scratch/test/FAL000870/f1.merged.cent_out.output.txt' +] + +[ + [ id: 'FAL00870', + strandedness: 'unstranded', + single_end: true, + centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab' + ], + '/hpc/scratch/test/FAL000870/f1.merged.cent_out.report.txt' +] +``` + +\ + + +#### `meta` + +Type: Groovy Map + +A Groovy Map containing the metadata about the FASTQ file. + +Ex: + +```groovy +[ + id: 'FAL00870', + strandedness: 'unstranded', + single_end: true, + centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab' +] +``` + +\ + + +#### `centrifuge_report` + +Type: `path` + +NextFlow input type of `path` pointing to `centrifuge` report file generated using `--report-file` option of `centrifuge` tool. + +\ + + +#### `centrifuge_output` + +Type: `path` + +NextFlow input type of `path` pointing to `centrifuge` output file generated using `-S` option of `centrifuge` tool. + +\ + + +### `output:` + +___ + +Type: `tuple` + +Outputs a tuple of metadata (`meta` from `input:`) and list of extracted FASTQ read ids. + +\ + + +#### `extracted` + +Type: `path` + +NextFlow output type of `path` pointing to the extracted FASTQ read ids belonging to a particular taxa (`*.extract-centrifuge-bug-ids.txt`). + +\ + + +#### `versions` + +Type: `path` + +NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/centrifuge/extract/main.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,59 @@ +process CENTRIFUGE_EXTRACT { + tag "$meta.id" + label 'process_low' + + //seqkit container contains required bash and other utilities + module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null) + conda (params.enable_conda ? "conda-forge::sed=4.7 conda-forge::coreutils" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mulled-v2-039542721b6b463b663872ba8b7e9fbc05f01925:1de88053ebf8fb9884758395c4871f642c57750c-0': + 'quay.io/biocontainers/mulled-v2-039542721b6b463b663872ba8b7e9fbc05f01925:1de88053ebf8fb9884758395c4871f642c57750c-0' }" + + input: + tuple val(meta), path(centrifuge_report) + tuple val(meta), path(centrifuge_output) + + output: + tuple val(meta), path('*.extract-centrifuge-bug-ids.txt'), emit: extracted + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + grep -F '${params.centrifuge_extract_bug}' $centrifuge_report \ + | cut -f2 \ + | sort -u \ + | while read -r taxId; do + echo -e "\t\$taxId"'\$' + done > gotcha.txt + + cut -f1-3 $centrifuge_output | grep -E -f gotcha.txt | cut -f1 | sort -u > ${prefix}.extract-centrifuge-bug-ids.txt || true + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bash: \$( bash --version 2>&1 | sed '1!d; s/^.*version //; s/ (.*\$//' ) + END_VERSIONS + + ver="" + sedver="" + + if [ "${workflow.containerEngine}" != "null" ]; then + ver=\$( cut --help 2>&1 | sed -e '1!d; s/ (.*\$//' ) + sedver="\$ver" + else + ver=\$( cut --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' ) + sedver=\$( echo \$(sed --version 2>&1) | sed 's/^.*(GNU sed) //; s/ Copyright.*\$//' ) + fi + + cat <<-END_VERSIONS >> versions.yml + cut: \$ver + tail: \$ver + sort: \$ver + sed: \$sedver + END_VERSIONS + """ +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/centrifuge/process/README.md Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,101 @@ +# NextFlow DSL2 Module + +```bash +CENTRIFUGE_PROCESS +``` + +## Description + +Extract FASTQ reads given a FASTQ file originally used with `centrifuge` tool and a taxa of interest. This specific module uses a `python` script to generate the FASTQ read ids and as such requires a `bin` folder with `process_centrifuge_output.py` to be present where the NextFlow script will be executed from. See also `CENTRIFUGE_EXTRACT` module which uses only GNU Coreutils to create a list of FASTQ read ids that need to be extracted. + +\ + + +### `input:` + +___ + +Type: `tuple` + +Takes in a tuple in order of metadata (`meta`), a `path` (`centrifuge_report`) type and another `path` (`centrifuge_report`) per sample (`id:`). + +Ex: + +```groovy +[ + [ id: 'FAL00870', + strandedness: 'unstranded', + single_end: true, + centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab' + ], + '/hpc/scratch/test/FAL000870/f1.merged.cent_out.report.txt', + '/hpc/scratch/test/FAL000870/f1.merged.cent_out.output.txt' +] +``` + +\ + + +#### `meta` + +Type: Groovy Map + +A Groovy Map containing the metadata about the FASTQ file. + +Ex: + +```groovy +[ + id: 'FAL00870', + strandedness: 'unstranded', + single_end: true, + centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab' +] +``` + +\ + + +#### `centrifuge_report` + +Type: `path` + +NextFlow input type of `path` pointing to `centrifuge` report file generated using `--report-file` option of `centrifuge` tool. + +\ + + +#### `centrifuge_output` + +Type: `path` + +NextFlow input type of `path` pointing to `centrifuge` output file generated using `-S` option of `centrifuge` tool. + +\ + + +### `output:` + +___ + +Type: `tuple` + +Outputs a tuple of metadata (`meta` from `input:`) and list of extracted FASTQ read ids. + +\ + + +#### `extracted` + +Type: `path` + +NextFlow output type of `path` pointing to the extracted FASTQ read ids belonging to a particular taxa (`*.extract-centrifuge-bug-ids.txt`). + +\ + + +#### `versions` + +Type: `path` + +NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/centrifuge/process/main.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,39 @@ +process CENTRIFUGE_PROCESS { + tag "$meta.id" + label 'process_low' + + module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null) + conda (params.enable_conda ? "conda-forge::python=3.9 conda-forge::pandas conda-forge::biopython" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mulled-v2-d91be2208450c41a5198d8660b6d9a5b60613b3a:d9847b41af5ef58746c86d7114cd010650f3d9a2-0' : + 'quay.io/biocontainers/mulled-v2-d91be2208450c41a5198d8660b6d9a5b60613b3a:d9847b41af5ef58746c86d7114cd010650f3d9a2-0' }" + + input: + tuple val(meta), path(centrifuge_report), path(centrifuge_output) + + output: + tuple val(meta), path('*.process-centrifuge-bug-ids.txt'), emit: extracted + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + process_centrifuge_output.py \\ + -r $centrifuge_report \\ + -o $centrifuge_output \\ + -b '${params.centrifuge_extract_bug}' \\ + -t ${prefix}.process-centrifuge-bug-ids.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + python: \$( python --version | sed 's/Python //g' ) + biopython: \$( python -c 'import Bio as bio; print(bio.__version__)' ) + numpy: \$( python -c 'import numpy as np; print(np.__version__)' ) + pandas: \$( python -c 'import pandas as pd; print(pd.__version__)' ) + END_VERSIONS + """ +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/custom/dump_software_versions/README.md Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,57 @@ +# NextFlow DSL2 Module + +```bash +DUMP_SOFTWARE_VERSIONS +``` + +## Description + +Given an `YAML` format file, produce a final `.yml` file which has unique entries and a corresponding `.mqc.yml` file for use with `multiqc`. + +\ + + +### `input:` + +___ + +Type: `path` + +Takes in a `path` (`versions`) type pointing to the file to be used to produce a final `.yml` file without any duplicate entries and a `.mqc.yml` file. Generally, this is passed by mixing `versions` from various run time channels and finally passed to this module to produce a final software versions list. + +Ex: + +```groovy +[ '/hpc/scratch/test/work/9b/e7bf7e28806419c1c9a571dacd1f67/versions.yml' ] +``` + +\ + + +### `output:` + +___ + +#### `yml` + +Type: `path` + +NextFlow output type of `path` type pointing to an `YAML` file with software versions. + +\ + + +#### `mqc_yml` + +Type: `path` + +NextFlow output type of `path` pointing to `.mqc.yml` file which can be used to produce a software versions' table with `multiqc`. + +\ + + +#### `versions` + +Type: `path` + +NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/custom/dump_software_versions/main.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,26 @@ +process DUMP_SOFTWARE_VERSIONS { + tag "${params.pipeline} software versions" + label 'process_pico' + + // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container + module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null) + conda (params.enable_conda ? "conda-forge::python=3.9 conda-forge::pyyaml" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mulled-v2-ca258a039fcd88610bc4e297b13703e8be53f5ca:d638c4f85566099ea0c74bc8fddc6f531fe56753-0' : + 'quay.io/biocontainers/mulled-v2-ca258a039fcd88610bc4e297b13703e8be53f5ca:d638c4f85566099ea0c74bc8fddc6f531fe56753-0' }" + + input: + path versions + + output: + path "software_versions.yml" , emit: yml + path "software_versions_mqc.yml", emit: mqc_yml + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + template 'dumpsoftwareversions.py' +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/custom/dump_software_versions/templates/dumpsoftwareversions.py Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,100 @@ +#!/usr/bin/env python + +import yaml +import platform +import subprocess +from textwrap import dedent + + +def _make_versions_html(versions): + html = [ + dedent( + """\\ + <link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/v/dt/jszip-2.5.0/dt-1.12.1/b-2.2.3/b-colvis-2.2.3/b-html5-2.2.3/b-print-2.2.3/fc-4.1.0/r-2.3.0/sc-2.0.6/sb-1.3.3/sp-2.0.1/datatables.min.css"/> + <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/pdfmake/0.1.36/pdfmake.min.js"></script> + <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/pdfmake/0.1.36/vfs_fonts.js"></script> + <script type="text/javascript" src="https://cdn.datatables.net/v/dt/jszip-2.5.0/dt-1.12.1/b-2.2.3/b-colvis-2.2.3/b-html5-2.2.3/b-print-2.2.3/fc-4.1.0/r-2.3.0/sc-2.0.6/sb-1.3.3/sp-2.0.1/datatables.min.js"></script> + <style> + #cpipes-software-versions tbody:nth-child(even) { + background-color: #f2f2f2; + } + </style> + <table class="table" style="width:100%" id="cpipes-software-versions"> + <thead> + <tr> + <th> Process Name </th> + <th> Software </th> + <th> Version </th> + </tr> + </thead> + """ + ) + ] + for process, tmp_versions in sorted(versions.items()): + html.append("<tbody>") + for i, (tool, version) in enumerate(sorted(tmp_versions.items())): + html.append( + dedent( + f"""\\ + <tr> + <td><samp>{process if (i == 0) else ''}</samp></td> + <td><samp>{tool}</samp></td> + <td><samp>{version}</samp></td> + </tr> + """ + ) + ) + html.append("</tbody>") + html.append("</table>") + return "\\n".join(html) + + +versions_this_module = {} +versions_this_module["${task.process}"] = { + "python": platform.python_version(), + "yaml": yaml.__version__, +} + +with open("$versions") as f: + versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) + versions_by_process.update(versions_this_module) + +# aggregate versions by the module name (derived from fully-qualified process name) +versions_by_module = {} +for process, process_versions in versions_by_process.items(): + module = process.split(":")[-1] + try: + assert versions_by_module[module] == process_versions, ( + "We assume that software versions are the same between all modules. " + "If you see this error-message it means you discovered an edge-case " + "and should open an issue in nf-core/tools. " + ) + except KeyError: + versions_by_module[module] = process_versions + +versions_by_module["CPIPES"] = { + "Nextflow": "$workflow.nextflow.version", + "$workflow.manifest.name": "$workflow.manifest.version", + "${params.pipeline}": "${params.workflow_version}" +} + +versions_mqc = { + "id": "software_versions", + "section_name": "${workflow.manifest.name} Software Versions", + "section_href": "https://cfsan-git.fda.gov/Kranti.Konganti/${workflow.manifest.name.toLowerCase()}", + "plot_type": "html", + "description": "Collected at run time from the software output (STDOUT/STDERR).", + "data": _make_versions_html(versions_by_module), +} + +with open("software_versions.yml", "w") as f: + yaml.dump(versions_by_module, f, default_flow_style=False) + +# print('sed -i -e "' + "s%'%%g" + '" *.yml') +subprocess.run('sed -i -e "' + "s%'%%g" + '" software_versions.yml', shell=True) + +with open("software_versions_mqc.yml", "w") as f: + yaml.dump(versions_mqc, f, default_flow_style=False) + +with open("versions.yml", "w") as f: + yaml.dump(versions_this_module, f, default_flow_style=False)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/ectyper/README.md Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,96 @@ +# NextFlow DSL2 Module + +```bash +ECTYPER +``` + +## Description + +Run `ectyper` tool on a list of assembled contigs in FASTA format. Produces a single output table in ASCII text format. + +\ + + +### `input:` + +___ + +Type: `tuple` + +Takes in the following tuple of metadata (`meta`) and a list of assemled contig FASTA files of input type `path` (`fasta`). + +Ex: + +```groovy +[ [id: 'sample1', single_end: true], '/data/sample1/f_assembly.fa' ] +``` + +\ + + +#### `meta` + +Type: Groovy Map + +A Groovy Map containing the metadata about the FASTQ file. + +Ex: + +```groovy +[ id: 'FAL00870', strandedness: 'unstranded', single_end: true ] +``` + +\ + + +#### `fasta` + +Type: `path` + +NextFlow input type of `path` pointing to assembled contig file in FASTA format. + +\ + + +#### `args` + +Type: Groovy String + +String of optional command-line arguments to be passed to the tool. This can be mentioned in `process` scope within `withName:process_name` block using `ext.args` option within your `nextflow.config` file. + +Ex: + +```groovy +withName: 'ECTYPER' { + ext.args = '--detailed' +} +``` + +\ + + +### `output:` + +___ + +Type: `tuple` + +Outputs a tuple of metadata (`meta` from `input:`) and list of `ectyper` result files (`ectyped`). + +\ + + +#### `ectyped` + +Type: `path` + +NextFlow output type of `path` pointing to the `ectyper` results table file per sample (`id:`). + +\ + + +#### `versions` + +Type: `path` + +NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/ectyper/main.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,45 @@ +process ECTYPER { + tag "$meta.id" + label 'process_low' + + module (params.enable_module ? "${params.swmodulepath}${params.fs}ectyper${params.fs}1.0.0" : null) + conda (params.enable_conda ? "bioconda::ectyper=1.0.0" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/ectyper:1.0.0--pyhdfd78af_1' : + 'quay.io/biocontainers/ectyper:1.0.0--pyhdfd78af_1' }" + + input: + tuple val(meta), path(fasta) + + output: + path("${meta.id}${params.fs}*") + tuple val(meta), path("${meta.id}${params.fs}${meta.id}.tsv"), emit: ectyped + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when || fasta.size() > 0 + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def is_compressed = fasta.getName().endsWith(".gz") ? true : false + def fasta_name = fasta.getName().replace(".gz", "") + """ + if [ "$is_compressed" == "true" ]; then + gzip -c -d $fasta > $fasta_name + fi + + ectyper \\ + $args \\ + --cores $task.cpus \\ + --output $prefix \\ + --input $fasta_name + + mv ${prefix}${params.fs}output.tsv ${prefix}${params.fs}${prefix}.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + ectyper: \$(echo \$(ectyper --version 2>&1) | sed 's/.*ectyper //; s/ .*\$//') + END_VERSIONS + """ +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/fastqc/README.md Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,113 @@ +# NextFlow DSL2 Module + +```bash +FASTQC +``` + +## Description + +Run `fastqc` tool on reads in FASTQ format. Produces a HTML report file and a `.zip` file containing plots and data used to produce the plots. + +\ + + +### `input:` + +___ + +Type: `tuple` + +Takes in the following tuple of metadata (`meta`) and a list of reads of type `path` (`reads`) per sample (`id:`). + +Ex: + +```groovy +[ + [ id: 'FAL00870', + strandedness: 'unstranded', + single_end: true, + centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab' + ], + '/hpc/scratch/test/FAL000870/f1.merged.fq.gz' +] +``` + +\ + + +#### `meta` + +Type: Groovy Map + +A Groovy Map containing the metadata about the FASTQ file. + +Ex: + +```groovy +[ + id: 'FAL00870', + strandedness: 'unstranded', + single_end: true +] +``` + +\ + + +#### `reads` + +Type: `path` + +NextFlow input type of `path` pointing to FASTQ files on which `fastqc` classification should be run. + +\ + + +#### `args` + +Type: Groovy String + +String of optional command-line arguments to be passed to the tool. This can be mentioned in `process` scope within `withName:process_name` block using `ext.args` option within your `nextflow.config` file. + +Ex: + +```groovy +withName: 'FASTQC' { + ext.args = '--nano' +} +``` + +### `output:` + +___ + +Type: `tuple` + +Outputs a tuple of metadata (`meta` from `input:`) and list of `fastqc` result files. + +\ + + +#### `html` + +Type: `path` + +NextFlow output type of `path` pointing to the `fastqc` report file in HTML format per sample (`id:`). + +\ + + +#### `zip` + +Type: `path` + +NextFlow output type of `path` pointing to the zipped `fastqc` results per sample (`id:`). + +\ + + +#### `versions` + +Type: `path` + +NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/fastqc/main.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,48 @@ +process FASTQC { + tag "$meta.id" + label 'process_low' + + module (params.enable_module ? "${params.swmodulepath}${params.fs}fastqc${params.fs}0.11.9" : null) + conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' : + 'quay.io/biocontainers/fastqc:0.11.9--0' }" + + input: + tuple val(meta), path(reads) + + output: + tuple val(meta), path("*.html"), emit: html + tuple val(meta), path("*.zip") , emit: zip + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + // Add soft-links to original FastQs for consistent naming in pipeline + def prefix = task.ext.prefix ?: "${meta.id}" + if (meta.single_end) { + """ + [ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz + fastqc $args --threads $task.cpus ${prefix}.fastq.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) + END_VERSIONS + """ + } else { + """ + [ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz + [ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz + fastqc $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) + END_VERSIONS + """ + } +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/flye/assemble/README.md Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,96 @@ +# NextFlow DSL2 Module + +```bash +FLYE_ASSEMBLE +``` + +## Description + +Run `flye` assembler tool on a list of read files in FASTQ format. + +\ + + +### `input:` + +___ + +Type: `tuple` + +Takes in the following tuple of metadata (`meta`) and a list of FASTQ files of input type `path` (`reads`). + +Ex: + +```groovy +[ [id: 'sample1', single_end: true], '/data/sample1/f_merged.fq.gz' ] +``` + +\ + + +#### `meta` + +Type: Groovy Map + +A Groovy Map containing the metadata about the FASTQ file. + +Ex: + +```groovy +[ id: 'FAL00870', strandedness: 'unstranded', single_end: true ] +``` + +\ + + +#### `reads` + +Type: `path` + +NextFlow input type of `path` pointing to read files in FASTQ format that need to be *de novo* assembled. + +\ + + +#### `args` + +Type: Groovy String + +String of optional command-line arguments to be passed to the tool. This can be mentioned in `process` scope within `withName:process_name` block using `ext.args` option within your `nextflow.config` file. + +Ex: + +```groovy +withName: 'FLYE_ASSEMBLE' { + ext.args = '--casava' +} +``` + +\ + + +### `output:` + +___ + +Type: `tuple` + +Outputs a tuple of metadata (`meta` from `input:`) and `flye` assembled contig file in FASTA format. + +\ + + +#### `assembly` + +Type: `path` + +NextFlow output type of `path` pointing to the `flye` assembler results file per sample (`id:`) i.e., the final assembled contig file in FASTA format. + +\ + + +#### `versions` + +Type: `path` + +NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/flye/assemble/main.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,51 @@ +process FLYE_ASSEMBLE { + tag "$meta.id" + label 'process_medium' + // errorStrategy 'ignore' + + module (params.enable_module ? "${params.swmodulepath}${params.fs}flye${params.fs}2.9" : null) + conda (params.enable_conda ? "bioconda::flye=2.9.0" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/flye:2.9--py38hf4f3596_1' : + 'quay.io/biocontainers/flye:2.9--py38hf4f3596_1' }" + + input: + tuple val(meta), path(reads) + + output: + path "${meta.id}${params.fs}*" + tuple val(meta), path("${meta.id}${params.fs}assembly.fasta"), emit: assembly, optional: true + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + """ + reads_platform=\$( echo "$args" | grep -E -o '(--nano|--pacbio)-(raw|corr|hq|hifi)' ) + flye \\ + \$(echo "$args" | sed -e "s/\$reads_platform//") \\ + -t $task.cpus \\ + --out-dir "${meta.id}" \\ + \$reads_platform \\ + $reads + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + flye: \$( flye --version ) + END_VERSIONS + + grepver="" + + if [ "${workflow.containerEngine}" != "null" ]; then + grepver=\$( grep --help 2>&1 | sed -e '1!d; s/ (.*\$//' ) + else + grepver=\$( echo \$( grep --version 2>&1 ) | sed 's/^.*(GNU grep) //; s/ Copyright.*\$//' ) + fi + + cat <<-END_VERSIONS >> versions.yml + grep: \$grepver + END_VERSIONS + """ +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/gen_samplesheet/README.md Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,55 @@ +# NextFlow DSL2 Module + +```bash +GEN_SAMPLESHEET +``` + +## Description + +Generates a sample sheet in CSV format that contains required fields to be used to construct a Groovy Map of metadata. It requires as input, an absolute UNIX path to a folder containing only FASTQ files. This module requires the `fastq_dir_to_samplesheet.py` script to be present in the `bin` folder from where the NextFlow script including this module will be executed. + +\ + + +### `input:` + +___ + +Type: `val` + +Takes in the absolute UNIX path to a folder containing only FASTQ files (`inputdir`). + +Ex: + +```groovy +'/hpc/scratch/test/reads' +``` + +\ + + +### `output:` + +___ + +Type: `path` + +NextFlow output of type `path` pointing to auto-generated CSV sample sheet (`csv`). + +\ + + +#### `csv` + +Type: `path` + +NextFlow output type of `path` pointing to auto-generated CSV sample sheet for all FASTQ files present in the folder given by NextFlow input type of `val` (`inputdir`). + +\ + + +#### `versions` + +Type: `path` + +NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/gen_samplesheet/main.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,41 @@ +process GEN_SAMPLESHEET { + tag "${inputdir.simpleName}" + label "process_pico" + + module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null) + conda (params.enable_conda ? "conda-forge::python=3.9.5" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/python:3.9--1' : + 'quay.io/biocontainers/python:3.9--1' }" + + input: + val inputdir + + output: + path '*.csv' , emit: csv + path 'versions.yml', emit: versions + + when: + task.ext.when == null || task.ext.when + + // This script (fastq_dir_to_samplesheet.py) is distributed + // as part of the pipeline nf-core/rnaseq/bin/. MIT License. + script: + def this_script_args = (params.fq_single_end ? ' -se' : '') + this_script_args += (params.fq_suffix ? " -r1 '${params.fq_suffix}'" : '') + this_script_args += (params.fq2_suffix ? " -r2 '${params.fq2_suffix}'" : '') + + """ + fastq_dir_to_samplesheet.py -sn \\ + -st '${params.fq_strandedness}' \\ + -sd '${params.fq_filename_delim}' \\ + -si ${params.fq_filename_delim_idx} \\ + ${this_script_args} \\ + ${inputdir} autogen_samplesheet.csv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + python: \$( python --version | sed 's/Python //g' ) + END_VERSIONS + """ +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/kraken2/classify/README.md Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,121 @@ +# NextFlow DSL2 Module + +```bash +KRAKEN2_CLASSIFY +``` + +## Description + +Run `kraken2` tool on reads in FASTQ format. Produces 4 output files per sample (`id:`) in ASCII text format. + +\ + + +### `input:` + +___ + +Type: `tuple` + +Takes in the following tuple of metadata (`meta`) and a list of reads or FASTA assembly of type `path` (`reads`) per sample (`id:`). + +Ex: + +```groovy +[ + [ id: 'FAL00870', + strandedness: 'unstranded', + single_end: true, + is_assembly: false, + centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab' + kraken2_db: '/hpc/db/kraken2/standard-210914', + ], + '/hpc/scratch/test/FAL000870/f1.merged.fq.gz' +] +``` + +\ + + +#### `meta` + +Type: Groovy Map + +A Groovy Map containing the metadata about the FASTQ / FASTA file. + +Ex: + +```groovy +[ + id: 'FAL00870', + strandedness: 'unstranded', + single_end: true, + is_assembly: false, + kraken2_db: '/hpc/db/kraken2/standard-210914' +] +``` + +\ + + +#### `reads` + +Type: `path` + +NextFlow input type of `path` pointing to FASTQ files on which `kraken2` classification should be run. + +\ + + +### `output:` + +___ + +Type: `tuple` + +Outputs a tuple of metadata (`meta` from `input:`) and list of `kraken2` result files. + +\ + + +#### `kraken_report` + +Type: `path` + +NextFlow output type of `path` pointing to the `kraken2` report table file (`.report.txt`) per sample (`id:`). + +\ + + +#### `kraken_output` + +Type: `path` + +NextFlow output type of `path` pointing to the `kraken2` output table file (`.output.txt`) per sample (`id:`). + +\ + + +#### `classified` + +Type: `path` + +NextFlow output type of `path` pointing to the `kraken2` processed gzipped FASTQ files containing only reads that have been classified (`*classified.fastq`) per sample (`id:`). + +\ + + +#### `unclassified` + +Type: `path` + +NextFlow output type of `path` pointing to the `kraken2` processed gzipped FASTQ files containing only reads that are unclassified (`*unclassified.fastq`) per sample (`id:`). + +\ + + +#### `versions` + +Type: `path` + +NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/kraken2/classify/main.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,73 @@ +process KRAKEN2_CLASSIFY { + tag "$meta.id" + label 'process_low' + + module (params.enable_module ? "${params.swmodulepath}${params.fs}kraken2${params.fs}2.1.2" : null) + conda (params.enable_conda ? 'bioconda::kraken2=2.1.2 conda-forge::pigz=2.6' : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0' : + 'quay.io/biocontainers/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0' }" + + input: + tuple val(meta), path(reads) + + output: + tuple val(meta), path('*classified*') , emit: classified + tuple val(meta), path('*unclassified*'), emit: unclassified + tuple val(meta), path('*.report.txt') , emit: kraken_report + tuple val(meta), path('*.output.txt') , emit: kraken_output + path "versions.yml" , emit: versions + + when: + (task.ext.when == null || task.ext.when) && (meta.is_assembly ? reads.size() : 1) + + script: + def args = task.ext.args ?: '' + def db = meta.kraken2_db ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def readList = reads.collect{ it.toString() } + def is_single_end = (meta.single_end || meta.is_assembly) ? true : false + def paired = is_single_end ? "" : "--paired" + def classified = is_single_end ? "--classified-out ${prefix}.classified.fastq" : "--classified-out ${prefix}.classified#.fastq" + def unclassified = is_single_end ? "--unclassified-out ${prefix}.unclassified.fastq" : "--unclassified-out ${prefix}.unclassified#.fastq" + args += (reads.getName().endsWith(".gz") ? ' --gzip-compressed ' : '') + """ + kraken2 \\ + --db $db \\ + --threads $task.cpus \\ + $unclassified \\ + $classified \\ + --report ${prefix}.kraken2.report.txt \\ + --output ${prefix}.kraken2.output.txt \\ + $paired \\ + $args \\ + $reads + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + kraken2: \$(echo \$(kraken2 --version 2>&1) | sed 's/^.*Kraken version //; s/ .*\$//') + END_VERSIONS + + zcmd="" + zver="" + + if type pigz > /dev/null 2>&1; then + pigz -p $task.cpus *.fastq + zcmd="pigz" + zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed -e '1!d' | sed "s/\$zcmd //" ) + elif type gzip > /dev/null 2>&1; then + gzip *.fastq + zcmd="gzip" + + if [ "${workflow.containerEngine}" != "null" ]; then + zver=\$( echo \$( \$zcmd --help 2>&1 ) | sed -e '1!d; s/ (.*\$//' ) + else + zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed "s/^.*(\$zcmd) //; s/\$zcmd //; s/ Copyright.*\$//" ) + fi + fi + + cat <<-END_VERSIONS >> versions.yml + \$zcmd: \$zver + END_VERSIONS + """ +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/kraken2/extract_contigs/README.md Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,101 @@ +# NextFlow DSL2 Module + +```bash +KRAKEN2_EXTRACT +``` + +## Description + +Extract FASTA reads or contigs given a FASTA file originally used with `kraken2` tool and a taxa of interest. This specific module uses a `python` script to generate the FASTA reads or contigs and as such requires a `bin` folder with `extract_assembled_filtered_contigs.py` script to be present where the NextFlow script will be executed from. + +\ + + +### `input:` + +___ + +Type: `tuple` + +Takes in a tuple in order of metadata (`meta`), a `path` (`kraken2_output`) type and another `path` (`assembly`) per sample (`id:`). + +Ex: + +```groovy +[ + [ id: 'FAL00870', + strandedness: 'unstranded', + single_end: true, + kraken2_db: '/hpc/db/kraken2/standard-210914' + ], + '/hpc/scratch/test/FAL000870/f1.merged.kraken2.output.txt', + '/hpc/scratch/test/FAL000870/f1.assembly.fasta' +] +``` + +\ + + +#### `meta` + +Type: Groovy Map + +A Groovy Map containing the metadata about the FASTA file. + +Ex: + +```groovy +[ + id: 'FAL00870', + strandedness: 'unstranded', + single_end: true, + kraken2_db: '/hpc/db/kraken2/standard-210914' +] +``` + +\ + + +#### `kraken2_output` + +Type: `path` + +NextFlow input type of `path` pointing to `kraken2` output file generated using `--output` option of `kraken2` tool. + +\ + + +#### `assembly` + +Type: `path` + +NextFlow input type of `path` pointing to a FASTA format file, in this case an assembled contig file in FASTA format. + +\ + + +### `output:` + +___ + +Type: `tuple` + +Outputs a tuple of metadata (`meta` from `input:`) and list of extracted FASTQ read ids. + +\ + + +#### `asm_filtered_contigs` + +Type: `path` + +NextFlow output type of `path` pointing to the extracted FASTA reads or contigs belonging to a particular taxa. + +\ + + +#### `versions` + +Type: `path` + +NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/kraken2/extract_contigs/main.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,40 @@ +process KRAKEN2_EXTRACT_CONTIGS { + tag "$meta.id" + label 'process_nano' + + module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null) + conda (params.enable_conda ? "conda-forge::python=3.9 conda-forge::pandas conda-forge::biopython" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mulled-v2-d91be2208450c41a5198d8660b6d9a5b60613b3a:d9847b41af5ef58746c86d7114cd010650f3d9a2-0' : + 'quay.io/biocontainers/mulled-v2-d91be2208450c41a5198d8660b6d9a5b60613b3a:d9847b41af5ef58746c86d7114cd010650f3d9a2-0' }" + + input: + tuple val(meta), path(assembly), path(kraken2_output) + val kraken2_extract_bug + + output: + tuple val(meta), path('*assembly_filtered_contigs.fasta'), emit: asm_filtered_contigs + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + extract_assembled_filtered_contigs.py \\ + -i $assembly \\ + -o ${prefix}.assembly_filtered_contigs.fasta \\ + -k $kraken2_output \\ + -b '$kraken2_extract_bug' + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + python: \$( python --version | sed 's/Python //g' ) + biopython: \$( python -c 'import Bio as bio; print(bio.__version__)' ) + numpy: \$( python -c 'import numpy as np; print(np.__version__)' ) + pandas: \$( python -c 'import pandas as pd; print(pd.__version__)' ) + END_VERSIONS + """ +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/megahit/assemble/README.md Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,97 @@ +# NextFlow DSL2 Module + +```bash +MEGAHIT_ASSEMBLE +``` + +## Description + +Run `megahit` assembler tool on a list of read files in FASTQ format. + +\ + + +### `input:` + +___ + +Type: `tuple` + +Takes in the following tuple of metadata (`meta`) and a list of FASTQ files (short reads) of input type `path` (`reads`). + +Ex: + +```groovy +[ [id: 'sample1', single_end: true], '/data/sample1/f_merged.fq.gz' ] +[ [id: 'sample1', single_end: false], ['/data/sample1/f1_merged.fq.gz', '/data/sample2/f2_merged.fq.gz'] ] +``` + +\ + + +#### `meta` + +Type: Groovy Map + +A Groovy Map containing the metadata about the FASTQ file. + +Ex: + +```groovy +[ id: 'KB01', strandedness: 'unstranded', single_end: true ] +``` + +\ + + +#### `reads` + +Type: `path` + +NextFlow input type of `path` pointing to short read files in FASTQ format that need to be *de novo* assembled. + +\ + + +#### `args` + +Type: Groovy String + +String of optional command-line arguments to be passed to the tool. This can be mentioned in `process` scope within `withName:process_name` block using `ext.args` option within your `nextflow.config` file. + +Ex: + +```groovy +withName: 'MEGAHIT_ASSEMBLE' { + ext.args = '--keep-tmp-files' +} +``` + +\ + + +### `output:` + +___ + +Type: `tuple` + +Outputs a tuple of metadata (`meta` from `input:`) and `megahit` assembled contigs file in FASTA format. + +\ + + +#### `assembly` + +Type: `path` + +NextFlow output type of `path` pointing to the `megahit` assembler results file (`final.contigs.fa`) per sample (`id:`) i.e., the final assembled contigs file in FASTA format. + +\ + + +#### `versions` + +Type: `path` + +NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/megahit/assemble/main.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,57 @@ +process MEGAHIT_ASSEMBLE { + tag "$meta.id" + label 'process_low' + + module (params.enable_module ? "${params.swmodulepath}${params.fs}megahit${params.fs}1.2.9" : null) + conda (params.enable_conda ? "bioconda::megahit=1.2.9" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/megahit:1.2.9--h2e03b76_1' : + 'quay.io/biocontainers/megahit:1.2.9--h2e03b76_1' }" + + input: + tuple val(meta), path(reads) + + output: + tuple val(meta), path("${meta.id}${params.fs}${meta.id}.contigs.fa"), emit: assembly, optional: true + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def maxmem = task.memory ? "--memory ${task.memory.toBytes()}" : "" + if (meta.single_end) { + """ + megahit \\ + -r ${reads} \\ + -t $task.cpus \\ + $maxmem \\ + $args \\ + --out-dir $prefix \\ + --out-prefix $prefix + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + megahit: \$(echo \$(megahit -v 2>&1) | sed 's/MEGAHIT v//') + END_VERSIONS + """ + } else { + """ + megahit \\ + -1 ${reads[0]} \\ + -2 ${reads[1]} \\ + -t $task.cpus \\ + $maxmem \\ + $args \\ + --out-dir $prefix \\ + --out-prefix $prefix + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + megahit: \$(echo \$(megahit -v 2>&1) | sed 's/MEGAHIT v//') + END_VERSIONS + """ + } +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/mlst/README.md Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,96 @@ +# NextFlow DSL2 Module + +```bash +MLST +``` + +## Description + +Run `mlst` tool on a list of assembled contigs in FASTA format. Produces a single output table in ASCII text format. + +\ + + +### `input:` + +___ + +Type: `tuple` + +Takes in the following tuple of metadata (`meta`) and a list of assemled contig FASTA files of input type `path` (`fasta`). + +Ex: + +```groovy +[ [id: 'sample1', single_end: true], '/data/sample1/f_assembly.fa' ] +``` + +\ + + +#### `meta` + +Type: Groovy Map + +A Groovy Map containing the metadata about the FASTQ file. + +Ex: + +```groovy +[ id: 'FAL00870', strandedness: 'unstranded', single_end: true ] +``` + +\ + + +#### `fasta` + +Type: `path` + +NextFlow input type of `path` pointing to assembled contig file in FASTA format. + +\ + + +#### `args` + +Type: Groovy String + +String of optional command-line arguments to be passed to the tool. This can be mentioned in `process` scope within `withName:process_name` block using `ext.args` option within your `nextflow.config` file. + +Ex: + +```groovy +withName: 'MLST' { + ext.args = '--nopath' +} +``` + +\ + + +### `output:` + +___ + +Type: `tuple` + +Outputs a tuple of metadata (`meta` from `input:`) and list of `mlst` result files (`tsv`). + +\ + + +#### `tsv` + +Type: `path` + +NextFlow output type of `path` pointing to the `mlst` results table file per sample (`id:`). + +\ + + +#### `versions` + +Type: `path` + +NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/mlst/main.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,36 @@ +process MLST { + tag "$meta.id" + label 'process_low' + + module (params.enable_module ? "${params.swmodulepath}${params.fs}mlst${params.fs}2.19.0" : null) + conda (params.enable_conda ? "bioconda::mlst=2.19.0" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mlst:2.19.0--hdfd78af_1' : + 'quay.io/biocontainers/mlst:2.19.0--hdfd78af_1' }" + + input: + tuple val(meta), path(fasta) + + output: + tuple val(meta), path("*.tsv"), emit: tsv + path "versions.yml" , emit: versions + + when: + (task.ext.when == null || task.ext.when) && fasta.size() > 0 + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + mlst \\ + --threads $task.cpus \\ + $args \\ + $fasta > ${prefix}.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + mlst: \$( echo \$(mlst --version 2>&1) | sed 's/mlst //' ) + END_VERSIONS + """ + +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/multiqc/README.md Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,67 @@ +# NextFlow DSL2 Module + +```bash +MULTIQC +``` + +## Description + +Generate an aggregated [**MultiQC**](https://multiqc.info/) report. This particular module **will only work** within the framework of `cpipes` as in, it uses many `cpipes` related UNIX absolute paths to store and retrieve **MultiQC** related configration files and `cpipes` context aware metadata. It also uses a custom logo with filename `FDa-Logo-Blue---medium-01.png` which should be located inside an `assets` folder from where the NextFlow script including this module will be executed. + +\ + + +### `input:` + +___ + +Type: `path` + +Takes in NextFlow input type of `path` which points to many log files that **MultiQC** should parse. + +Ex: + +```groovy +[ '/data/sample1/centrifuge/cent_output.txt', '/data/sample1/kraken/kraken_output.txt'] ] +``` + +\ + + +### `output:` + +___ + +#### `report` + +Type: `path` + +Outputs a NextFlow output type of `path` pointing to the location of **MultiQC** final HTML report. + +\ + + +#### `data` + +Type: `path` + +NextFlow output type of `path` pointing to the data files folder generated by **MultiQC** which were used to generate plots and HTML report. + +\ + + +#### `plots` + +Type: `path` +Optional: `true` + +NextFlow output type of `path` pointing to the plots folder generated by **MultiQC**. + +\ + + +#### `versions` + +Type: `path` + +NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/multiqc/main.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,52 @@ +process MULTIQC { + label 'process_micro' + tag 'MultiQC' + + module (params.enable_module ? "${params.swmodulepath}${params.fs}multiqc${params.fs}1.19" : null) + conda (params.enable_conda ? 'conda-forge::python=3.11 conda-forge::spectra conda-forge::lzstring conda-forge::imp bioconda::multiqc=1.19' : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' : + 'quay.io/biocontainers/multiqc:1.19--pyhdfd78af_0' }" + + input: + path multiqc_files + + output: + path "*multiqc*" + path "*multiqc_report.html", emit: report + path "*_data" , emit: data + path "*_plots" , optional: true, emit: plots + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + """ + cp ${params.projectconf}${params.fs}multiqc${params.fs}${params.pipeline}_mqc.yml cpipes_mqc_config.yml + cp ${params.assetsdir}${params.fs}FDa-Logo-Blue---medium-01.png FDa-Logo-Blue---medium-01.png + sed -i -e 's/Workflow_Name_Placeholder/${params.pipeline}/g; s/Workflow_Version_Placeholder/${params.workflow_version}/g' cpipes_mqc_config.yml + sed -i -e 's/CPIPES_Version_Placeholder/${workflow.manifest.version}/g; s%Workflow_Output_Placeholder%${params.output}%g' cpipes_mqc_config.yml + sed -i -e 's%Workflow_Input_Placeholder%${params.input}%g' cpipes_mqc_config.yml + + multiqc -c cpipes_mqc_config.yml -f $args . + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) + END_VERSIONS + + sedver="" + + if [ "${workflow.containerEngine}" != "null" ]; then + sedver=\$( sed --help 2>&1 | sed -e '1!d; s/ (.*\$//' ) + else + sedver=\$( echo \$(sed --version 2>&1) | sed 's/^.*(GNU sed) //; s/ Copyright.*\$//' ) + fi + + cat <<-END_VERSIONS >> versions.yml + sed: \$sedver + END_VERSIONS + """ +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/samplesheet_check/README.md Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,55 @@ +# NextFlow DSL2 Module + +```bash +SAMPLESHEET_CHECK +``` + +## Description + +Checks the validity of the sample sheet in CSV format to make sure there are required mandatory fields. This module generally succeeds `GEN_SAMPLESHEET` module as part of the `cpipes` pipelines to make sure that all fields of the columns are properly formatted to be used as Groovy Map for `meta` which is of input type `val`. This module requires the `check_samplesheet.py` script to be present in the `bin` folder from where the NextFlow script including this module will be executed + +\ + + +### `input:` + +___ + +Type: `path` + +Takes in the absolute UNIX path to the sample sheet in CSV format (`samplesheet`). + +Ex: + +```groovy +'/hpc/scratch/test/reads/output/gen_samplesheet/autogen_samplesheet.csv' +``` + +\ + + +### `output:` + +___ + +Type: `path` + +NextFlow output of type `path` pointing to properly formatted CSV sample sheet (`csv`). + +\ + + +#### `csv` + +Type: `path` + +NextFlow output type of `path` pointing to auto-generated CSV sample sheet for all FASTQ files present in the folder given by NextFlow input type of `val` (`inputdir`). + +\ + + +#### `versions` + +Type: `path` + +NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/samplesheet_check/main.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,32 @@ +process SAMPLESHEET_CHECK { + tag "$samplesheet" + label "process_femto" + + module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null) + conda (params.enable_conda ? "conda-forge::python=3.9.5" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/python:3.9--1' : + 'quay.io/biocontainers/python:3.9--1' }" + + input: + path samplesheet + + output: + path '*.csv' , emit: csv + path "versions.yml", emit: versions + + when: + task.ext.when == null || task.ext.when + + script: // This script is bundled with the pipeline, in nf-core/rnaseq/bin/ + """ + check_samplesheet.py \\ + $samplesheet \\ + samplesheet.valid.csv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + python: \$( python --version | sed 's/Python //g' ) + END_VERSIONS + """ +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/seqkit/grep/README.md Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,113 @@ +# NextFlow DSL2 Module + +```bash +SEQKIT_GREP +``` + +## Description + +Run `seqkit grep` command on reads in FASTQ format. Produces a filtered FASTQ file as per the filter strategy in the supplied input file. + +\ + + +### `input:` + +___ + +Type: `tuple` + +Takes in the following tuple of metadata (`meta`) and a list of reads of type `path` (`reads`) per sample (`id:`). + +Ex: + +```groovy +[ + [ id: 'FAL00870', + strandedness: 'unstranded', + single_end: true, + centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab' + ], + '/hpc/scratch/test/FAL000870/f1.merged.fq.gz' +] +``` + +\ + + +#### `meta` + +Type: Groovy Map + +A Groovy Map containing the metadata about the FASTQ file. + +Ex: + +```groovy +[ + id: 'FAL00870', + strandedness: 'unstranded', + single_end: true +] +``` + +\ + + +#### `reads` + +Type: `path` + +NextFlow input type of `path` pointing to FASTQ files on which `seqkit grep` should be run. + +\ + + +#### `pattern_file` + +Type: path + +NextFlow input type of `path` pointing to the pattern file which has the patterns, one per line, by which FASTQ sequence ids should be searched and whose reads will be extracted. + +\ + + +#### `args` + +Type: Groovy String + +String of optional command-line arguments to be passed to the tool. This can be mentioned in `process` scope within `withName:process_name` block using `ext.args` option within your `nextflow.config` file. + +Ex: + +```groovy +withName: 'SEQKIT_GREP' { + ext.args = '--only-positive-strand' +} +``` + +### `output:` + +___ + +Type: `tuple` + +Outputs a tuple of metadata (`meta` from `input:`) and and filtered gzipped FASTQ file. + +\ + + +#### `fastx` + +Type: `path` + +NextFlow output type of `path` pointing to the FASTQ format filtered gzipped file per sample (`id:`). + +\ + + +#### `versions` + +Type: `path` + +NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/seqkit/grep/main.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,89 @@ +process SEQKIT_GREP { + tag "$meta.id" + label 'process_low' + + module (params.enable_module ? "${params.swmodulepath}${params.fs}seqkit${params.fs}2.2.0" : null) + conda (params.enable_conda ? "bioconda::seqkit=2.2.0 conda-forge::sed=4.7 conda-forge::coreutils" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/seqkit:2.1.0--h9ee0642_0': + 'quay.io/biocontainers/seqkit:2.1.0--h9ee0642_0' }" + + input: + tuple val(meta), path(reads), path(pattern_file) + + output: + tuple val(meta), path("*.gz"), emit: fastx + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + + def extension = "fastq" + if ("$reads" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz/) { + extension = "fasta" + } + + if (meta.single_end) { + """ + pattern_file_contents=\$(sed '1!d' $pattern_file) + if [ "\$pattern_file_contents" != "DuMmY" ]; then + additional_args="-f $pattern_file $args" + else + additional_args="$args" + fi + + seqkit \\ + grep \\ + -j $task.cpus \\ + -o ${prefix}.seqkit-grep.${extension}.gz \\ + \$additional_args \\ + $reads + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + seqkit: \$( seqkit | sed '3!d; s/Version: //' ) + END_VERSIONS + """ + } else { + """ + pattern_file_contents=\$(sed '1!d' $pattern_file) + if [ "\$pattern_file_contents" != "DuMmY" ]; then + additional_args="-f $pattern_file $args" + else + additional_args="$args" + fi + + seqkit \\ + grep \\ + -j $task.cpus \\ + -o ${prefix}.R1.seqkit-grep.${extension}.gz \\ + \$additional_args \\ + ${reads[0]} + + seqkit \\ + grep \\ + -j $task.cpus \\ + -o ${prefix}.R2.seqkit-grep.${extension}.gz \\ + \$additional_args \\ + ${reads[1]} + + seqkit \\ + pair \\ + -j $task.cpus \\ + -1 ${prefix}.R1.seqkit-grep.${extension}.gz \\ + -2 ${prefix}.R2.seqkit-grep.${extension}.gz + + rm ${prefix}.R1.seqkit-grep.${extension}.gz + rm ${prefix}.R2.seqkit-grep.${extension}.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + seqkit: \$( seqkit | sed '3!d; s/Version: //' ) + END_VERSIONS + """ + } +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/seqkit/rmdup/README.md Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,104 @@ +# NextFlow DSL2 Module + +```bash +SEQKIT_RMDUP +``` + +## Description + +Run `seqkit rmdup` command on reads in FASTQ format. Produces a filtered FASTQ file without duplicate sequences as per the strategy set using `ext.args` within the process scope. + +\ + + +### `input:` + +___ + +Type: `tuple` + +Takes in the following tuple of metadata (`meta`) and a list of reads of type `path` (`reads`) per sample (`id:`). + +Ex: + +```groovy +[ + [ id: 'FAL00870', + strandedness: 'unstranded', + single_end: true, + centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab' + ], + '/hpc/scratch/test/FAL000870/f1.merged.fq.gz' +] +``` + +\ + + +#### `meta` + +Type: Groovy Map + +A Groovy Map containing the metadata about the FASTQ file. + +Ex: + +```groovy +[ + id: 'FAL00870', + strandedness: 'unstranded', + single_end: true +] +``` + +\ + + +#### `reads` + +Type: `path` + +NextFlow input type of `path` pointing to FASTQ files on which `seqkit rmdup` should be run. + +\ + + +#### `args` + +Type: Groovy String + +String of optional command-line arguments to be passed to the tool. This can be mentioned in `process` scope within `withName:process_name` block using `ext.args` option within your `nextflow.config` file. + +Ex: + +```groovy +withName: 'SEQKIT_DUP' { + ext.args = '-t dna' +} +``` + +### `output:` + +___ + +Type: `tuple` + +Outputs a tuple of metadata (`meta` from `input:`) and filtered gzipped FASTQ file. + +\ + + +#### `fastx` + +Type: `path` + +NextFlow output type of `path` pointing to the FASTQ format filtered gzipped file per sample (`id:`). + +\ + + +#### `versions` + +Type: `path` + +NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/seqkit/rmdup/main.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,84 @@ +process SEQKIT_RMDUP { + tag "$meta.id" + label 'process_low' + + module (params.enable_module ? "${params.swmodulepath}${params.fs}seqkit${params.fs}2.2.0" : null) + conda (params.enable_conda ? "bioconda::seqkit=2.2.0" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/seqkit:2.1.0--h9ee0642_0': + 'quay.io/biocontainers/seqkit:2.1.0--h9ee0642_0' }" + + input: + tuple val(meta), path(reads) + + output: + tuple val(meta), path("*duplicated.details.txt"), optional: true + tuple val(meta), path("*.gz") , emit: fastx + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def rmdup_d = params.seqkit_rmdup_d ? "-d ${prefix}.seqs.duplicated.fastq.gz" : "" + def rmdup_D = params.seqkit_rmdup_D ? "-D ${prefix}.duplicated.details.txt" : "" + + def extension = "fastq" + if ("$reads" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz/) { + extension = "fasta" + } + + if (meta.single_end) { + """ + seqkit \\ + rmdup \\ + $rmdup_d \\ + $rmdup_D \\ + -j $task.cpus \\ + -o ${prefix}.seqkit-rmdup.${extension}.gz \\ + $args \\ + $reads + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + seqkit: \$( seqkit | sed '3!d; s/Version: //' ) + END_VERSIONS + """ + } else { + """ + seqkit \\ + rmdup \\ + $rmdup_d \\ + $rmdup_D \\ + -j $task.cpus \\ + -o ${prefix}.R1.seqkit-rmdup.${extension}.gz \\ + $args \\ + ${reads[0]} + + seqkit \\ + rmdup \\ + $rmdup_d \\ + $rmdup_D \\ + -j $task.cpus \\ + -o ${prefix}.R2.seqkit-rmdup.${extension}.gz \\ + $args \\ + ${reads[1]} + + seqkit \\ + pair \\ + -j $task.cpus \\ + -1 ${prefix}.R1.seqkit-rmdup.${extension}.gz \\ + -2 ${prefix}.R2.seqkit-rmdup.${extension}.gz + + rm ${prefix}.R1.seqkit-rmdup.${extension}.gz + rm ${prefix}.R2.seqkit-rmdup.${extension}.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + seqkit: \$( seqkit | sed '3!d; s/Version: //' ) + END_VERSIONS + """ + } +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/seqkit/seq/README.md Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,104 @@ +# NextFlow DSL2 Module + +```bash +SEQKIT_SEQ +``` + +## Description + +Run `seqkit seq` command on reads in FASTQ format. Produces a filtered FASTQ file as per the filter strategy mentioned using the `ext.args` within the process scope. + +\ + + +### `input:` + +___ + +Type: `tuple` + +Takes in the following tuple of metadata (`meta`) and a list of reads of type `path` (`reads`) per sample (`id:`). + +Ex: + +```groovy +[ + [ id: 'FAL00870', + strandedness: 'unstranded', + single_end: true, + centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab' + ], + '/hpc/scratch/test/FAL000870/f1.merged.fq.gz' +] +``` + +\ + + +#### `meta` + +Type: Groovy Map + +A Groovy Map containing the metadata about the FASTQ file. + +Ex: + +```groovy +[ + id: 'FAL00870', + strandedness: 'unstranded', + single_end: true +] +``` + +\ + + +#### `reads` + +Type: `path` + +NextFlow input type of `path` pointing to FASTQ files on which `seqkit seq` should be run. + +\ + + +#### `args` + +Type: Groovy String + +String of optional command-line arguments to be passed to the tool. This can be mentioned in `process` scope within `withName:process_name` block using `ext.args` option within your `nextflow.config` file. + +Ex: + +```groovy +withName: 'SEQKIT_SEQ' { + ext.args = '--max-len 4000' +} +``` + +### `output:` + +___ + +Type: `tuple` + +Outputs a tuple of metadata (`meta` from `input:`) and filtered gzipped FASTQ file. + +\ + + +#### `fastx` + +Type: `path` + +NextFlow output type of `path` pointing to the FASTQ format filtered gzipped file per sample (`id:`). + +\ + + +#### `versions` + +Type: `path` + +NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/seqkit/seq/main.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,75 @@ +process SEQKIT_SEQ { + tag "$meta.id" + label 'process_low' + + module (params.enable_module ? "${params.swmodulepath}${params.fs}seqkit${params.fs}2.2.0" : null) + conda (params.enable_conda ? "bioconda::seqkit=2.2.0" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/seqkit:2.1.0--h9ee0642_0': + 'quay.io/biocontainers/seqkit:2.1.0--h9ee0642_0' }" + + input: + tuple val(meta), path(reads) + + output: + tuple val(meta), path("*.gz"), emit: fastx + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + + def extension = "fastq" + if ("$reads" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz/) { + extension = "fasta" + } + + if (meta.single_end) { + """ + seqkit \\ + seq \\ + -j $task.cpus \\ + -o ${prefix}.seqkit-seq.${extension}.gz \\ + $args \\ + $reads + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + seqkit: \$( seqkit | sed '3!d; s/Version: //' ) + END_VERSIONS + """ + } else { + """ + seqkit \\ + seq \\ + -j $task.cpus \\ + -o ${prefix}.R1.seqkit-seq.${extension}.gz \\ + $args \\ + ${reads[0]} + + seqkit \\ + seq \\ + -j $task.cpus \\ + -o ${prefix}.R2.seqkit-seq.${extension}.gz \\ + $args \\ + ${reads[1]} + + seqkit \\ + pair \\ + -j $task.cpus \\ + -1 ${prefix}.R1.seqkit-seq.${extension}.gz \\ + -2 ${prefix}.R2.seqkit-seq.${extension}.gz + + rm ${prefix}.R1.seqkit-seq.${extension}.gz + rm ${prefix}.R2.seqkit-seq.${extension}.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + seqkit: \$( seqkit | sed '3!d; s/Version: //' ) + END_VERSIONS + """ + } +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/seqsero2/README.md Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,96 @@ +# NextFlow DSL2 Module + +```bash +SEQSERO2 +``` + +## Description + +Run `seqsero2` tool on a list of assembled *Salmonella* contigs in FASTA format or sequencing reads in FASTQ format. + +\ + + +### `input:` + +___ + +Type: `tuple` + +Takes in the following tuple of metadata (`meta`) and a list of assemled contig FASTA files or list of sequencing reads in FASTQ format of input type `path` (`reads_or_asm`). + +Ex: + +```groovy +[ [id: 'sample1', single_end: true], '/data/sample1/f_assembly.fa' ] +``` + +\ + + +#### `meta` + +Type: Groovy Map + +A Groovy Map containing the metadata about the FASTQ files or assembly FASTA files. + +Ex: + +```groovy +[ id: 'FAL00870', strandedness: 'unstranded', single_end: true ] +``` + +\ + + +#### `reads_or_asm` + +Type: `path` + +NextFlow input type of `path` pointing to assembled contig file in FASTA format or sequencing reads in FASTQ format. + +\ + + +#### `args` + +Type: Groovy String + +String of optional command-line arguments to be passed to the tool. This can be mentioned in `process` scope within `withName:process_name` block using `ext.args` option within your `nextflow.config` file. + +Ex: + +```groovy +withName: 'SEQSERO2' { + ext.args = '-b mem' +} +``` + +\ + + +### `output:` + +___ + +Type: `tuple` + +Outputs a tuple of metadata (`meta` from `input:`) and list of `seqsero2` result files (`serotyped`). + +\ + + +#### `serotyped` + +Type: `path` + +NextFlow output type of `path` pointing to the `seqsero2` results table file per sample (`id:`). + +\ + + +#### `versions` + +Type: `path` + +NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/seqsero2/main.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,42 @@ +process SEQSERO2 { + tag "$meta.id" + label 'process_low' + + module (params.enable_module ? "${params.swmodulepath}${params.fs}seqsero2${params.fs}1.2.1" : null) + conda (params.enable_conda ? "bioconda::seqsero2=1.2.1" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/seqsero2:1.2.1--py_0' : + 'quay.io/biocontainers/seqsero2:1.2.1--py_0' }" + + input: + tuple val(meta), path(reads_or_asm) + + output: + path("${meta.id}${params.fs}*") + tuple val(meta), path("${meta.id}${params.fs}*_result.tsv"), emit: serotyped + path "versions.yml" , emit: versions + + when: + (task.ext.when == null || task.ext.when) && reads_or_asm.size() > 0 + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + SeqSero2_package.py \\ + $args \\ + -d $prefix \\ + -n $prefix \\ + -p $task.cpus \\ + -i $reads_or_asm + + mv ${prefix}${params.fs}SeqSero_log.txt ${prefix}${params.fs}${prefix}.SeqSero_log.txt + mv ${prefix}${params.fs}SeqSero_result.txt ${prefix}${params.fs}${prefix}.SeqSero_result.txt + mv ${prefix}${params.fs}SeqSero_result.tsv ${prefix}${params.fs}${prefix}.SeqSero_result.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + seqsero2: \$( echo \$( SeqSero2_package.py --version 2>&1) | sed 's/^.*SeqSero2_package.py //' ) + END_VERSIONS + """ +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/seqtk/seq/README.md Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,104 @@ +# NextFlow DSL2 Module + +```bash +SEQTK_SEQ +``` + +## Description + +Run `seqtk seq` command on reads in FASTQ format. Produces a filtered FASTQ file as per the filter strategy mentioned using the `ext.args` within the process scope. Please note that `seqtk seq` works only on one FASTQ file per command call. For paired-end reads, please use the `SEQKIT_SEQ` module. + +\ + + +### `input:` + +___ + +Type: `tuple` + +Takes in the following tuple of metadata (`meta`) and a list of reads of type `path` (`reads`) per sample (`id:`). + +Ex: + +```groovy +[ + [ id: 'FAL00870', + strandedness: 'unstranded', + single_end: true, + centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab' + ], + '/hpc/scratch/test/FAL000870/f1.merged.fq.gz' +] +``` + +\ + + +#### `meta` + +Type: Groovy Map + +A Groovy Map containing the metadata about the FASTQ file. + +Ex: + +```groovy +[ + id: 'FAL00870', + strandedness: 'unstranded', + single_end: true +] +``` + +\ + + +#### `reads` + +Type: `path` + +NextFlow input type of `path` pointing to FASTQ files on which `seqtk seq` should be run. + +\ + + +#### `args` + +Type: Groovy String + +String of optional command-line arguments to be passed to the tool. This can be mentioned in `process` scope within `withName:process_name` block using `ext.args` option within your `nextflow.config` file. + +Ex: + +```groovy +withName: 'SEQTK_SEQ' { + ext.args = '-L 4000' +} +``` + +### `output:` + +___ + +Type: `tuple` + +Outputs a tuple of metadata (`meta` from `input:`) and filtered gzipped FASTQ file. + +\ + + +#### `fastx` + +Type: `path` + +NextFlow output type of `path` pointing to the FASTQ format filtered gzipped file per sample (`id:`). + +\ + + +#### `versions` + +Type: `path` + +NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/seqtk/seq/main.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,42 @@ +process SEQTK_SEQ { + tag "$meta.id" + label 'process_mem_low' + + module (params.enable_module ? "${params.swmodulepath}${params.fs}seqtk${params.fs}1.3-r106" : null) + conda (params.enable_conda ? "bioconda::seqtk=1.3 conda-forge::gzip" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' : + 'quay.io/biocontainers/seqtk:1.3--h5bf99c6_3' }" + + input: + tuple val(meta), path(fastx) + + output: + tuple val(meta), path("*.gz"), emit: fastx + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + + def extension = "fastq" + if ("$fastx" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz/ || "$args" ==~ /\-[aA]/ ) { + extension = "fasta" + } + """ + seqtk \\ + seq \\ + $args \\ + $fastx | \\ + gzip -c > ${prefix}.seqtk-seq.${task.index}.${extension}.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + seqtk: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//') + gzip: \$( echo \$(gzip --version 2>&1) | sed 's/^.*(gzip) //; s/gzip //; s/ Copyright.*\$//' ) + END_VERSIONS + """ +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/serotypefinder/README.md Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,96 @@ +# NextFlow DSL2 Module + +```bash +SEROTYPEFINDER +``` + +## Description + +Run `serotypefinder` tool on a list of assembled *E. coli* contigs or partial sequences in FASTA format. Produces a single output table in ASCII text format. + +\ + + +### `input:` + +___ + +Type: `tuple` + +Takes in the following tuple of metadata (`meta`) and a list of assemled contig FASTA files of input type `path` (`fasta`). + +Ex: + +```groovy +[ [id: 'sample1', single_end: true], '/data/sample1/f_assembly.fa' ] +``` + +\ + + +#### `meta` + +Type: Groovy Map + +A Groovy Map containing the metadata about the assembly FASTA file. + +Ex: + +```groovy +[ id: 'FAL00870', strandedness: 'unstranded', single_end: true ] +``` + +\ + + +#### `fasta` + +Type: `path` + +NextFlow input type of `path` pointing to assembled contig file or partial sequences in FASTA format. + +\ + + +#### `args` + +Type: Groovy String + +String of optional command-line arguments to be passed to the tool. This can be mentioned in `process` scope within `withName:process_name` block using `ext.args` option within your `nextflow.config` file. + +Ex: + +```groovy +withName: 'SEROTYPEFINDER' { + ext.args = '-mp kma' +} +``` + +\ + + +### `output:` + +___ + +Type: `tuple` + +Outputs a tuple of metadata (`meta` from `input:`) and list of `serotypefinder` result files (`serotyped`). + +\ + + +#### `serotyped` + +Type: `path` + +NextFlow output type of `path` pointing to the `serotypefinder` results table file per sample (`id:`). + +\ + + +#### `versions` + +Type: `path` + +NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/serotypefinder/main.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,70 @@ +process SEROTYPEFINDER { + tag "$meta.id" + label 'process_low' + + module (params.enable_module ? "${params.swmodulepath}${params.fs}serotypefinder${params.fs}2.0.2" : null) + conda (params.enable_conda ? "bioconda::serotypefinder=2.0.1" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/serotypefinder:2.0.1--py39hdfd78af_0' : + 'quay.io/biocontainers/serotypefinder:2.0.1--py39hdfd78af_0' }" + + input: + tuple val(meta), path(fasta) + + output: + path("${meta.id}${params.fs}*") + tuple val(meta), path("${meta.id}${params.fs}${meta.id}.tsv"), emit: serotyped + path "versions.yml" , emit: versions + + when: + (task.ext.when == null || task.ext.when) && fasta.size() > 0 + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def is_compressed = fasta.getName().endsWith(".gz") ? true : false + def fasta_name = fasta.getName().replace(".gz", "") + def serotypefinder_db = "${meta.serotypefinder_db}" + def serotypefinder_cmd = (params.enable_module ? "serotypefinder.py" : "serotypefinder") + """ + if [ "$is_compressed" == "true" ]; then + gzip -c -d $fasta > $fasta_name + fi + + mkdir -p $prefix > /dev/null 2>&1 + + $serotypefinder_cmd \\ + $args \\ + -p $serotypefinder_db \\ + -o $prefix \\ + -i $fasta_name + + head -n1 ${prefix}${params.fs}results_tab.tsv | sed -E "s/(.*)/Name\\t\\1/g" > ${prefix}${params.fs}${prefix}.tsv + tail -n+2 ${prefix}${params.fs}results_tab.tsv | sed -E "s/(.*)/${prefix}\\t\\1/g" >> ${prefix}${params.fs}${prefix}.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + serotypefinder: 2.0.1/2.0.2 + END_VERSIONS + + sedver="" + headver="" + tailver="" + + if [ "${workflow.containerEngine}" != "null" ]; then + sedver=\$( sed --help 2>&1 | sed -e '1!d; s/ (.*\$//' ) + headver=\$( head --help 2>&1 | sed -e '1!d; s/ (.*\$//' ) + tailver="\$headver" + else + sedver=\$( echo \$(sed --version 2>&1) | sed 's/^.*(GNU sed) //; s/ Copyright.*\$//' ) + headver=\$( head --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' ) + tailver=\$( tail --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' ) + fi + + cat <<-END_VERSIONS >> versions.yml + sed: \$sedver + head: \$headver + tail: \$tailver + END_VERSIONS + """ +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/spades/assemble/README.md Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,115 @@ +# NextFlow DSL2 Module + +```bash +SPADES_ASSEMBLE +``` + +## Description + +Run `spades` assembler tool on a list of read files in FASTQ format. + +\ + + +### `input:` + +___ + +Type: `tuple` + +Takes in the following tuple of metadata (`meta`) and a list of FASTQ files from various platforms of input type `path` (`illumina`, `pacbio`, `nanopore`). + +Ex: + +```groovy +[ [id: 'sample1', single_end: true], '/data/sample1/f_merged.fq.gz' ] +[ [id: 'sample1', single_end: false], ['/data/sample1/f1_merged.fq.gz', '/data/sample2/f2_merged.fq.gz'], ['/data/sample1/nanopore.fastq'], ['/data/sample1/pacbio.fastq'] ] +``` + +\ + + +#### `meta` + +Type: Groovy Map + +A Groovy Map containing the metadata about the FASTQ file. + +Ex: + +```groovy +[ id: 'FAL00870', strandedness: 'unstranded', single_end: true ] +``` + +\ + + +#### `illumina` + +Type: `path` + +NextFlow input type of `path` pointing to Illumina read files in FASTQ format that need to be *de novo* assembled along with reads from any other sequencing platforms, if any. + +\ + + +#### `nanopore` + +Type: `path` + +NextFlow input type of `path` pointing to Oxford Nanopore read files in FASTQ format that need to be *de novo* assembled along with reads from any other sequencing platforms, if any. + +\ + + +#### `pacbio` + +Type: `path` + +NextFlow input type of `path` pointing to PacBio read files in FASTQ format that need to be *de novo* assembled along with reads from any other sequencing platforms, if any. + +\ + + +#### `args` + +Type: Groovy String + +String of optional command-line arguments to be passed to the tool. This can be mentioned in `process` scope within `withName:process_name` block using `ext.args` option within your `nextflow.config` file. + +Ex: + +```groovy +withName: 'SPADES_ASSEMBLE' { + ext.args = '--rna' +} +``` + +\ + + +### `output:` + +___ + +Type: `tuple` + +Outputs a tuple of metadata (`meta` from `input:`) and `spades` assembled scaffolds file in FASTA format. + +\ + + +#### `assembly` + +Type: `path` + +NextFlow output type of `path` pointing to the `spades` assembler results file (`scaffolds.fasta`) per sample (`id:`) i.e., the final assembled scaffolds file in FASTA format. + +\ + + +#### `versions` + +Type: `path` + +NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/modules/spades/assemble/main.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,47 @@ +process SPADES_ASSEMBLE { + tag "$meta.id" + label 'process_higher' + + module (params.enable_module ? "${params.swmodulepath}${params.fs}spades${params.fs}3.15.3" : null) + conda (params.enable_conda ? 'bioconda::spades=3.15.3' : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/spades:3.15.3--h95f258a_0' : + 'quay.io/biocontainers/spades:3.15.3--h95f258a_0' }" + + input: + tuple val(meta), path(illumina), path(pacbio), path(nanopore) + + output: + path "${meta.id}${params.fs}*" + tuple val(meta), path("${meta.id}${params.fs}scaffolds.fasta"), emit: assembly, optional: true + tuple val(meta), path("${meta.id}${params.fs}spades.log") , emit: log + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def maxmem = task.memory ? "--memory ${task.memory.toGiga()}" : "" + def illumina_reads = illumina ? ( meta.single_end ? "-s $illumina" : "-1 ${illumina[0]} -2 ${illumina[1]}" ) : "" + def pacbio_reads = !(pacbio.simpleName ==~ 'dummy_file.*') ? "--pacbio $pacbio" : "" + def nanopore_reads = !(nanopore.simpleName ==~ 'dummy_file.*') ? "--nanopore $nanopore" : "" + def custom_hmms = params.spades_hmm ? "--custom-hmms ${params.spades_hmm}" : "" + """ + spades.py \\ + $args \\ + --threads $task.cpus \\ + $maxmem \\ + $custom_hmms \\ + $illumina_reads \\ + $pacbio_reads \\ + $nanopore_reads \\ + -o ${prefix} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + spades: \$(spades.py --version 2>&1 | sed 's/^.*SPAdes genome assembler v//; s/ .*\$//') + END_VERSIONS + """ +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/nextflow.config Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,38 @@ +def fs = File.separator +def pd = "${projectDir}" + +// Global parameters +includeConfig "${pd}${fs}conf${fs}manifest.config" +includeConfig "${pd}${fs}conf${fs}base.config" + +// Include FASTQ config to prepare for a case when the entry point is +// FASTQ metadata CSV or FASTQ input directory +includeConfig "${pd}${fs}conf${fs}fastq.config" + +if (params.pipeline != null) { + try { + includeConfig "${params.workflowsconf}${fs}${params.pipeline}.config" + } catch (Exception e) { + System.err.println('-'.multiply(params.linewidth) + "\n" + + "\033[0;31m${params.cfsanpipename} - ERROR\033[0m\n" + + '-'.multiply(params.linewidth) + "\n" + "\033[0;31mCould not load " + + "default pipeline configuration. Please provide a pipeline \n" + + "name using the --pipeline option.\n\033[0m" + '-'.multiply(params.linewidth) + "\n") + System.exit(1) + } +} + +// Include modules' config last. +includeConfig "${pd}${fs}conf${fs}logtheseparams.config" +includeConfig "${pd}${fs}conf${fs}modules.config" + +// Nextflow runtime profiles +conda.cacheDir = "${pd}${fs}kondagac_cache" +singularity.cacheDir = "${pd}${fs}cingularitygac_cache" + +// Cleanup after running +cleanup = true + +profiles { + includeConfig "${pd}${fs}conf${fs}computeinfra.config" +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/readme/centriflaken.md Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,858 @@ +# centriflaken + +`centriflaken` is an automated precision metagenomics workflow for assembly and _in silico_ analyses of food-borne pathogens. `centriflaken` primarily fine-tuned for detecting and classifying Shiga toxin-producing **_Escherichia coli_** (**STEC**), can also be used for performing analyses on other food-borne pathogens such as **_Salmonella enterica_**. `centriflaken` takes as input a UNIX path to FASTQ, generates MAGs, and performs in silico-based analysis for STECs as described in [Maguire et al. 2021](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0245172). + +`centriflaken` works on both **Illumina** short reads and **Oxford Nanopore** long reads. + +It is written in **Nextflow** and is part of the modular data analysis pipelines at **HFP**. + +\ + + +<!-- TOC --> + +- [Minimum Requirements](#minimum-requirements) +- [HFP GalaxyTrakr](#hfp-galaxytrakr) +- [Usage and Examples](#usage-and-examples) + - [Databases](#databases) + - [Input](#input) + - [Illumina short reads](#illumina-short-reads) + - [Output](#output) + - [Computational resources](#computational-resources) + - [Runtime profiles](#runtime-profiles) + - [your_institution.config](#your_institutionconfig) + - [Test run](#test-run) +- [centriflaken CLI Help](#centriflaken-cli-help) +- [centriflaken_hy CLI Help](#centriflaken_hy-cli-help) + +<!-- /TOC --> + +\ + + +## Minimum Requirements + +1. [Nextflow version 24.10.4](https://github.com/nextflow-io/nextflow/releases/download/v24.10.4/nextflow). + - Make the `nextflow` binary executable (`chmod 755 nextflow`) and also make sure that it is made available in your `$PATH`. + - If your existing `JAVA` install does not support the newest **Nextflow** version, you can try **Amazon**'s `JAVA` (OpenJDK): [Corretto](https://docs.aws.amazon.com/corretto/latest/corretto-21-ug/downloads-list.html). +2. Either of `micromamba` (version `1.5.9`) or `docker` or `singularity` installed and made available in your `$PATH`. + - Running the workflow via `micromamba` software provisioning is **preferred** as it does not require any `sudo` or `admin` privileges or any other configurations with respect to the various container providers. + - To install `micromamba` for your system type, please follow these [installation steps](https://mamba.readthedocs.io/en/latest/installation/micromamba-installation.html#linux-and-macos) and make sure that the `micromamba` binary is made available in your `$PATH`. + - Just the `curl` step is sufficient to download the binary as far as running the workflows are concerned. + - Once you have finished the installation, **it is important that you downgrade `micromamba` to version `1.5.9`**. + - First check, if your version is other than `1.5.9` and if not, do the downgrade. + + ```bash + micromamba --version + micromamba self-update --version 1.5.9 -c conda-forge + ``` + +3. Minimum of 10 CPU cores and about 60 GBs for main workflow steps. More memory may be required if your **FASTQ** files are big. + +\ + + +## HFP GalaxyTrakr + +The `centriflaken` pipeline is also available for use on the [Galaxy instance supported by HFP, FDA](https://galaxytrakr.org/). If you wish to run the analysis using **Galaxy**, please register for an account, after which [you can run the workflow using this protocol](https://www.protocols.io/view/centriflaken-an-automated-data-analysis-pipeline-f-kxygxzdbwv8j/v5). + +Please note that the pipeline on [HFP GalaxyTrakr](https://galaxytrakr.org) in most cases may be a version older than the one on **GitHub** due to testing prioritization. + +\ + + +## Usage and Examples + +Clone or download this repository and then call `cpipes`. + +```bash +cpipes --pipeline centriflaken [options] +``` + +Alternatively, you can use `nextflow` to directly pull and run the pipeline. + +```bash +nextflow pull CFSAN-Biostatistics/centriflaken +nextflow list +nextflow info CFSAN-Biostatistics/centriflaken +nextflow run CFSAN-Biostatistics/centriflaken --pipeline centriflaken --help +nextflow run CFSAN-Biostatistics/centriflaken --pipeline centriflaken_hy --help +``` + +\ + + +### Databases + +--- + +The successful run of the workflow requires all of the following databases: + +- `kraken2`, `centrifuge`, `serotypefinder` and `abricate`: [Download](https://cfsan-pub-xfer.s3.amazonaws.com/Kranti.Konganti/centriflaken/centriflaken_dbs.tar.bz2). + +Once you have downloaded the databases, uncompress and set the **UNIX** path's in the configuration files as follows: + +- [Line no. 4](../workflows/conf/centriflaken.config#L4): `centrifuge_x = /path/to/centriflaken_dbs/centrifuge/ab`. The `ab` prefix is necessary. +- [Line no. 11](../workflows/conf/centriflaken_hy.config#L11): `centrifuge_x = /path/to/centriflaken_dbs/centrifuge/ab`. The `ab` prefix is necessary. +- [Line no. 10](../workflows/conf/centriflaken.config#L10): `kraken2_db = /path/to/centriflaken_dbs/kraken2`. +- [Line no. 17](../workflows/conf/centriflaken_hy.config#L17): `kraken2_db = /path/to/centriflaken_dbs/kraken2`. +- [Line no. 36](../workflows/conf/centriflaken.config#L36): `serotypefinder_db = /path/to/centriflaken_dbs/serotypefinder`. +- [Line no. 64](../workflows/conf/centriflaken_hy.config#L64): `serotypefinder_db = /path/to/centriflaken_dbs/serotypefinder`. +- [Line no. 53](../workflows/conf/centriflaken.config#L53): `abricate_datadir = /path/to/centriflaken_dbs/abricate`. +- [Line no. 81](../workflows/conf/centriflaken_hy.config#L81): `abricate_datadir = /path/to/centriflaken_dbs/abricate`. + +\ + + +### Input + +--- + +The input to the workflow is a folder containing compressed (`.gz`) FASTQ files of long reads or short reads. Please note that the sample grouping happens automatically by the file name of the FASTQ file. If for example, a single sample is sequenced across multiple sequencing lanes, you can choose to group those FASTQ files into one sample by using the `--fq_filename_delim` and `--fq_filename_delim_idx` options. By default, `--fq_filename_delim` is set to `_` (underscore) and `--fq_filename_delim_idx` is set to 1. + +For example, if the directory contains FASTQ files as shown below: + +- KB-01_apple_L001_R1.fastq.gz +- KB-01_apple_L001_R2.fastq.gz +- KB-01_apple_L002_R1.fastq.gz +- KB-01_apple_L002_R2.fastq.gz +- KB-02_mango_L001_R1.fastq.gz +- KB-02_mango_L001_R2.fastq.gz +- KB-02_mango_L002_R1.fastq.gz +- KB-02_mango_L002_R2.fastq.gz + +Then, to create 2 sample groups, `apple` and `mango`, we split the file name by the delimitor (underscore in the case, which is default) and group by the first 2 words (`--fq_filename_delim_idx 2`). + +This goes without saying that all the FASTQ files should have uniform naming patterns so that `--fq_filename_delim` and `--fq_filename_delim_idx` options do not have any adverse effect in collecting and creating a sample metadata sheet. + +\ + + +### Illumina short reads + +--- + +`centriflaken` was primarily developed for **ONT** long reads but also supports **Illumina** short reads. Use the `--pipeline centriflaken_hy` instead of `--pipeline centriflaken` to activate this feature. The `centriflaken_hy` variant of the pipeline uses `megahit` instead of `flye` to perform short read assembly. There is no other change needed from the user other than using the `--pipeline centriflaken_hy` parameter for Illumina short reads. + +\ + + +### Output + +--- + +All the outputs for each step are stored inside the folder mentioned with the `--output` option. A `multiqc_report.html` file inside the `centriflaken-multiqc` folder can be opened in any browser on your local workstation which contains a consolidated brief report. + +\ + + +### Computational resources + +--- + +The workflows `centriflaken` and `centriflaken_hy` require at least a minimum of 60 GBs of memory to successfully finish the workflow. + +\ + + +### Runtime profiles + +--- + +You can use different run time profiles that suit your specific compute environments i.e., you can run the workflow locally on your machine or in a grid computing infrastructure. + +\ + + +Example: + +```bash +cd /data/scratch/$USER +mkdir nf-cpipes +cd nf-cpipes +cpipes \ + --pipeline centriflaken \ + --input /path/to/fastq_pass_dir \ + --output /path/to/where/output/should/go \ + -profile your_institution +``` + +The above command would run the pipeline and store the output at the location per the `--output` flag and the **NEXTFLOW** reports are always stored in the current working directory from where `cpipes` is run. For example, for the above command, a directory called `CPIPES-centriflaken` would hold all the **NEXTFLOW** related logs, reports and trace files. + +\ + + +### `your_institution.config` + +--- + +In the above example, we can see that we have mentioned the run time profile as `your_institution`. For this to work, add the following lines at the end of [`computeinfra.config`](../conf/computeinfra.config) file which should be located inside the `conf` folder. For example, if your institution uses **SGE** or **UNIVA** for grid computing instead of **SLURM** and has a job queue named `normal.q`, then add these lines: + +\ + + +```groovy +your_institution { + process.executor = 'sge' + process.queue = 'normal.q' + singularity.enabled = false + singularity.autoMounts = true + docker.enabled = false + params.enable_conda = true + conda.enabled = true + conda.useMicromamba = true + params.enable_module = false +} +``` + +In the above example, by default, all the software provisioning choices are disabled except `conda`. You can also choose to remove the `process.queue` line altogether and the `centriflaken` workflow will request the appropriate memory and number of CPU cores automatically, which ranges from 1 CPU, 1 GB and 1 hour for job completion up to 10 CPU cores, 1 TB and 120 hours for job completion. + +\ + + +### Cloud computing + +--- + +You can run the workflow in the cloud (works only with proper set up of AWS resources). Add new run time profiles with required parameters per [Nextflow docs](https://www.nextflow.io/docs/latest/executor.html): + +\ + + +Example: + +```groovy +my_aws_batch { + executor = 'awsbatch' + queue = 'my-batch-queue' + aws.batch.cliPath = '/home/ec2-user/miniconda/bin/aws' + aws.batch.region = 'us-east-1' + singularity.enabled = false + singularity.autoMounts = true + docker.enabled = true + params.conda_enabled = false + params.enable_module = false +} +``` + +\ + + +### Test run + +--- + +After you make sure that you have all the [minimum requirements](#minimum-requirements) to run the workflow, you can try the `centriflaken` pipeline on some subsampled reads belonging to the NCBI BioProject `PRJNA639799` as discussed in [Maguire _et al_](https://pmc.ncbi.nlm.nih.gov/articles/PMC10500926/). + +- Please note that the input reads are subsampled to validate the software install. +- Download them [from S3](https://cfsan-pub-xfer.s3.amazonaws.com/Kranti.Konganti/centriflaken/macguire_et_al_subsampled_reads.tar.bz2) (~ 20 GB). + + | Samples | Biosample | SRA accession | Flowcell | + |:---------------------------------------------------------------|:-------------|:--------------|:---------| + | FAL00958 | SAMN46790801 | SRR32346290 | FAL00958 | + | FAL01198 | SAMN46793213 | SRR32346289 | FAL01198 | + | FAL01556 | SAMN46793220 | SRR32346278 | FAL01556 | + | ZymoBIOMICS Microbial Community DNA Standard R1 | SAMN46793392 | SRR32381322 | FAL11413 | + | ZymoBIOMICS Microbial Community DNA Standard R2 | SAMN46793393 | SRR32381321 | FAL01565 | + | ZymoBIOMICS Microbial Community Standard II - log distribution | SAMN46793397 | SRR32381320 | FAL01514 | + +- Download pre-formatted databases (**MANDATORY**) [from S3](https://cfsan-pub-xfer.s3.amazonaws.com/Kranti.Konganti/centriflaken/centriflaken_dbs.tar.bz2) (~ 47 GB). +- One of the assembly jobs should fail to assemble the reads and the pipeline will ignore the failed assembly and finish to completion. +- After successful download, untar and change the paths to the databases in **BOTH** the [long reads conf file](../workflows/conf/centriflaken.config) and [short reads conf file](../workflows/conf/centriflaken_hy.config) as described in the [Databases](#databases) section. +- The following values should point to the UNIX paths of the downloaded databases. + + ```bash + centrifuge_x = '/path/to/centrifuge/ab' # /ab suffix SHOULD NOT change. Only the /path/to/centrifuge changes to your specific UNIX path. + kraken2_db = '/path/to/kraken2' + serotypefinder_db = '/path/to/serotypefinder' + abricate_datadir = '/path/to/abricate' + amrfinderplus_db = '/hpc/db/amrfinderplus/3.10.24/latest' # IGNORE THIS PATH SINCE AMRFINDERPLUS SHOULD NOT BE RUN. + ``` + +- It is always a best practice to use absolute UNIX paths and real destinations of symbolic links during pipeline execution. For example, find out the real path(s) of your absolute UNIX path(s) and use that for the `--input` and `--output` options of the pipeline. + + ```bash + realpath /hpc/scratch/user/input/srr + ``` + +- Now run the workflow by ignoring quality values since these are simulated base qualities: + + ```bash + cpipes \ + --pipeline centriflaken \ + --input /path/to/macguire_et_al_subsampled_reads \ + --output /path/to/centriflaken_test_output \ + -profile stdkondagac \ + -resume + ``` + +- After succesful run of the workflow, your **MultiQC** report should look something like [this](https://cfsan-pub-xfer.s3.us-east-1.amazonaws.com/Kranti.Konganti/centriflaken/macquire_et_al_test_report.html). + +Please note that the run time profile `stdkondagac` will run jobs locally using `micromamba` for software provisioning. The first time you run the command, a new folder called `kondagac_cache` will be created and subsequent runs should use this `conda` cache. + +\ + + +## `centriflaken` CLI Help + +```text +cpipes --pipeline centriflaken --help + + N E X T F L O W ~ version 24.10.4 + +Launching `/home/user/centriflaken/cpipes` [sleepy_pauling] DSL2 - revision: 55d6f63710 + +================================================================================ + (o) + ___ _ __ _ _ __ ___ ___ + / __|| '_ \ | || '_ \ / _ \/ __| +| (__ | |_) || || |_) || __/\__ \ + \___|| .__/ |_|| .__/ \___||___/ + | | | | + |_| |_| +-------------------------------------------------------------------------------- +A collection of modular pipelines at CFSAN, FDA. +-------------------------------------------------------------------------------- +Name : CPIPES +Author : Kranti.Konganti@fda.hhs.gov +Version : 0.4.1 +Center : CFSAN, FDA. +================================================================================ + +Workflow : centriflaken + +Author : Kranti.Konganti@fda.hhs.gov + +Version : 0.4.2 + + +Usage : cpipes --pipeline centriflaken [options] + + +Required : + +--input : Absolute path to directory containing FASTQ + files. The directory should contain only + FASTQ files as all the files within the + mentioned directory will be read. Ex: -- + input /path/to/fastq_pass + +--output : Absolute path to directory where all the + pipeline outputs should be stored. Ex: -- + output /path/to/output + +Other options : + +--metadata : Absolute path to metadata CSV file + containing five mandatory columns: sample, + fq1,fq2,strandedness,single_end. The fq1 + and fq2 columns contain absolute paths to + the FASTQ files. This option can be used in + place of --input option. This is rare. Ex: -- + metadata samplesheet.csv + +--fq_suffix : The suffix of FASTQ files (Unpaired reads + or R1 reads or Long reads) if an input + directory is mentioned via --input option. + Default: .fastq.gz + +--fq2_suffix : The suffix of FASTQ files (Paired-end reads + or R2 reads) if an input directory is + mentioned via --input option. Default: + false + +--fq_filter_by_len : Remove FASTQ reads that are less than this + many bases. Default: 4000 + +--fq_strandedness : The strandedness of the sequencing run. + This is mostly needed if your sequencing + run is RNA-SEQ. For most of the other runs, + it is probably safe to use unstranded for + the option. Default: unstranded + +--fq_single_end : SINGLE-END information will be auto- + detected but this option forces PAIRED-END + FASTQ files to be treated as SINGLE-END so + only read 1 information is included in auto- + generated samplesheet. Default: false + +--fq_filename_delim : Delimiter by which the file name is split + to obtain sample name. Default: _ + +--fq_filename_delim_idx : After splitting FASTQ file name by using + the --fq_filename_delim option, all + elements before this index (1-based) will + be joined to create final sample name. + Default: 1 + +--kraken2_db : Absolute path to kraken database. Default: / + hpc/db/kraken2/standard-210914 + +--kraken2_confidence : Confidence score threshold which must be + between 0 and 1. Default: 0.0 + +--kraken2_quick : Quick operation (use first hit or hits). + Default: false + +--kraken2_use_mpa_style : Report output like Kraken 1's kraken-mpa- + report. Default: false + +--kraken2_minimum_base_quality : Minimum base quality used in classification + which is only effective with FASTQ input. + Default: 0 + +--kraken2_report_zero_counts : Report counts for ALL taxa, even if counts + are zero. Default: false + +--kraken2_report_minmizer_data : Report minimizer and distinct minimizer + count information in addition to normal + Kraken report. Default: false + +--kraken2_use_names : Print scientific names instead of just + taxids. Default: true + +--kraken2_extract_bug : Extract the reads or contigs beloging to + this bug. Default: Escherichia coli + +--centrifuge_x : Absolute path to centrifuge database. + Default: /hpc/db/centrifuge/2022-04-12/ab + +--centrifuge_save_unaligned : Save SINGLE-END reads that did not align. + For PAIRED-END reads, save read pairs that + did not align concordantly. Default: false + +--centrifuge_save_aligned : Save SINGLE-END reads that aligned. For + PAIRED-END reads, save read pairs that + aligned concordantly. Default: false + +--centrifuge_out_fmt_sam : Centrifuge output should be in SAM. Default: + false + +--centrifuge_extract_bug : Extract this bug from centrifuge results. + Default: Escherichia coli + +--centrifuge_ignore_quals : Treat all quality values as 30 on Phred + scale. Default: false + +--flye_pacbio_raw : Input FASTQ reads are PacBio regular CLR + reads (<20% error) Defaut: false + +--flye_pacbio_corr : Input FASTQ reads are PacBio reads that + were corrected with other methods (<3% + error). Default: false + +--flye_pacbio_hifi : Input FASTQ reads are PacBio HiFi reads (<1% + error). Default: false + +--flye_nano_raw : Input FASTQ reads are ONT regular reads, + pre-Guppy5 (<20% error). Default: true + +--flye_nano_corr : Input FASTQ reads are ONT reads that were + corrected with other methods (<3% error). + Default: false + +--flye_nano_hq : Input FASTQ reads are ONT high-quality + reads: Guppy5+ SUP or Q20 (<5% error). + Default: false + +--flye_genome_size : Estimated genome size (for example, 5m or 2. + 6g). Default: 5.5m + +--flye_polish_iter : Number of genome polishing iterations. + Default: false + +--flye_meta : Do a metagenome assembly (unenven coverage + mode). Default: true + +--flye_min_overlap : Minimum overlap between reads. Default: + false + +--flye_scaffold : Enable scaffolding using assembly graph. + Default: false + +--serotypefinder_run : Run SerotypeFinder tool. Default: true + +--serotypefinder_x : Generate extended output files. Default: + true + +--serotypefinder_db : Path to SerotypeFinder databases. Default: / + hpc/db/serotypefinder/2.0.2 + +--serotypefinder_min_threshold : Minimum percent identity (in float) + required for calling a hit. Default: 0.85 + +--serotypefinder_min_cov : Minumum percent coverage (in float) + required for calling a hit. Default: 0.80 + +--seqsero2_run : Run SeqSero2 tool. Default: false + +--seqsero2_t : '1' for interleaved paired-end reads, '2' + for separated paired-end reads, '3' for + single reads, '4' for genome assembly, '5' + for nanopore reads (fasta/fastq). Default: + 4 + +--seqsero2_m : Which workflow to apply, 'a'(raw reads + allele micro-assembly), 'k'(raw reads and + genome assembly k-mer). Default: k + +--seqsero2_c : SeqSero2 will only output serotype + prediction without the directory containing + log files. Default: false + +--seqsero2_s : SeqSero2 will not output header in + SeqSero_result.tsv. Default: false + +--mlst_run : Run MLST tool. Default: true + +--mlst_minid : DNA %identity of full allelle to consider ' + similar' [~]. Default: 95 + +--mlst_mincov : DNA %cov to report partial allele at all [?]. + Default: 10 + +--mlst_minscore : Minumum score out of 100 to match a scheme. + Default: 50 + +--abricate_run : Run ABRicate tool. Default: true + +--abricate_minid : Minimum DNA %identity. Defaut: 90 + +--abricate_mincov : Minimum DNA %coverage. Defaut: 80 + +--abricate_datadir : ABRicate databases folder. Defaut: /hpc/db/ + abricate/1.0.1/db + +Help options : + +--help : Display this message. +``` + +\ + + +## `centriflaken_hy` CLI Help + +```text +cpipes --pipeline centriflaken_hy --help + + N E X T F L O W ~ version 24.10.4 + +Launching `/home/user/centriflaken/cpipes` [big_ramanujan] DSL2 - revision: 55d6f63710 + +================================================================================ + (o) + ___ _ __ _ _ __ ___ ___ + / __|| '_ \ | || '_ \ / _ \/ __| +| (__ | |_) || || |_) || __/\__ \ + \___|| .__/ |_|| .__/ \___||___/ + | | | | + |_| |_| +-------------------------------------------------------------------------------- +A collection of modular pipelines at CFSAN, FDA. +-------------------------------------------------------------------------------- +Name : CPIPES +Author : Kranti.Konganti@fda.hhs.gov +Version : 0.4.1 +Center : CFSAN, FDA. +================================================================================ + +Workflow : centriflaken_hy + +Author : Kranti.Konganti@fda.hhs.gov + +Version : 0.4.1 + + +Usage : cpipes --pipeline centriflaken_hy [options] + + +Required : + +--input : Absolute path to directory containing FASTQ + files. The directory should contain only + FASTQ files as all the files within the + mentioned directory will be read. Ex: -- + input /path/to/fastq_pass + +--output : Absolute path to directory where all the + pipeline outputs should be stored. Ex: -- + output /path/to/output + +Other options : + +--metadata : Absolute path to metadata CSV file + containing five mandatory columns: sample, + fq1,fq2,strandedness,single_end. The fq1 + and fq2 columns contain absolute paths to + the FASTQ files. This option can be used in + place of --input option. This is rare. Ex: -- + metadata samplesheet.csv + +--fq_suffix : The suffix of FASTQ files (Unpaired reads + or R1 reads or Long reads) if an input + directory is mentioned via --input option. + Default: _R1_001.fastq.gz + +--fq2_suffix : The suffix of FASTQ files (Paired-end reads + or R2 reads) if an input directory is + mentioned via --input option. Default: + _R2_001.fastq.gz + +--fq_filter_by_len : Remove FASTQ reads that are less than this + many bases. Default: 75 + +--fq_strandedness : The strandedness of the sequencing run. + This is mostly needed if your sequencing + run is RNA-SEQ. For most of the other runs, + it is probably safe to use unstranded for + the option. Default: unstranded + +--fq_single_end : SINGLE-END information will be auto- + detected but this option forces PAIRED-END + FASTQ files to be treated as SINGLE-END so + only read 1 information is included in auto- + generated samplesheet. Default: false + +--fq_filename_delim : Delimiter by which the file name is split + to obtain sample name. Default: _ + +--fq_filename_delim_idx : After splitting FASTQ file name by using + the --fq_filename_delim option, all + elements before this index (1-based) will + be joined to create final sample name. + Default: 1 + +--seqkit_rmdup_run : Remove duplicate sequences using seqkit + rmdup. Default: false + +--seqkit_rmdup_n : Match and remove duplicate sequences by + full name instead of just ID. Defaut: false + +--seqkit_rmdup_s : Match and remove duplicate sequences by + sequence content. Defaut: true + +--seqkit_rmdup_d : Save the duplicated sequences to a file. + Defaut: false + +--seqkit_rmdup_D : Save the number and list of duplicated + sequences to a file. Defaut: false + +--seqkit_rmdup_i : Ignore case while using seqkit rmdup. + Defaut: false + +--seqkit_rmdup_P : Only consider positive strand (i.e. 5') + when comparing by sequence content. Defaut: + false + +--kraken2_db : Absolute path to kraken database. Default: / + hpc/db/kraken2/standard-210914 + +--kraken2_confidence : Confidence score threshold which must be + between 0 and 1. Default: 0.0 + +--kraken2_quick : Quick operation (use first hit or hits). + Default: false + +--kraken2_use_mpa_style : Report output like Kraken 1's kraken-mpa- + report. Default: false + +--kraken2_minimum_base_quality : Minimum base quality used in classification + which is only effective with FASTQ input. + Default: 0 + +--kraken2_report_zero_counts : Report counts for ALL taxa, even if counts + are zero. Default: false + +--kraken2_report_minmizer_data : Report minimizer and distinct minimizer + count information in addition to normal + Kraken report. Default: false + +--kraken2_use_names : Print scientific names instead of just + taxids. Default: true + +--kraken2_extract_bug : Extract the reads or contigs beloging to + this bug. Default: Escherichia coli + +--centrifuge_x : Absolute path to centrifuge database. + Default: /hpc/db/centrifuge/2022-04-12/ab + +--centrifuge_save_unaligned : Save SINGLE-END reads that did not align. + For PAIRED-END reads, save read pairs that + did not align concordantly. Default: false + +--centrifuge_save_aligned : Save SINGLE-END reads that aligned. For + PAIRED-END reads, save read pairs that + aligned concordantly. Default: false + +--centrifuge_out_fmt_sam : Centrifuge output should be in SAM. Default: + false + +--centrifuge_extract_bug : Extract this bug from centrifuge results. + Default: Escherichia coli + +--centrifuge_ignore_quals : Treat all quality values as 30 on Phred + scale. Default: false + +--megahit_run : Run MEGAHIT assembler. Default: true + +--megahit_min_count : <int>. Minimum multiplicity for filtering ( + k_min+1)-mers. Defaut: false + +--megahit_k_list : Comma-separated list of kmer size. All + values must be odd, in the range 15-255, + increment should be <= 28. Ex: '21,29,39,59, + 79,99,119,141'. Default: false + +--megahit_no_mercy : Do not add mercy k-mers. Default: false + +--megahit_bubble_level : <int>. Intensity of bubble merging (0-2), 0 + to disable. Default: false + +--megahit_merge_level : <l,s>. Merge complex bubbles of length <= l* + kmer_size and similarity >= s. Default: + false + +--megahit_prune_level : <int>. Strength of low depth pruning (0-3). + Default: false + +--megahit_prune_depth : <int>. Remove unitigs with avg k-mer depth + less than this value. Default: false + +--megahit_low_local_ratio : <float>. Ratio threshold to define low + local coverage contigs. Default: false + +--megahit_max_tip_len : <int>. remove tips less than this value [< + int> * k]. Default: false + +--megahit_no_local : Disable local assembly. Default: false + +--megahit_kmin_1pass : Use 1pass mode to build SdBG of k_min. + Default: false + +--megahit_preset : <str>. Override a group of parameters. + Valid values are meta-sensitive which + enforces '--min-count 1 --k-list 21,29,39, + 49,...,129,141', meta-large (large & + complex metagenomes, like soil) which + enforces '--k-min 27 --k-max 127 --k-step + 10'. Default: meta-sensitive + +--megahit_mem_flag : <int>. SdBG builder memory mode. 0: minimum; + 1: moderate; 2: use all memory specified. + Default: 2 + +--megahit_min_contig_len : <int>. Minimum length of contigs to output. + Default: false + +--spades_run : Run SPAdes assembler. Default: false + +--spades_isolate : This flag is highly recommended for high- + coverage isolate and multi-cell data. + Defaut: false + +--spades_sc : This flag is required for MDA (single-cell) + data. Default: false + +--spades_meta : This flag is required for metagenomic data. + Default: true + +--spades_bio : This flag is required for biosytheticSPAdes + mode. Default: false + +--spades_corona : This flag is required for coronaSPAdes mode. + Default: false + +--spades_rna : This flag is required for RNA-Seq data. + Default: false + +--spades_plasmid : Runs plasmidSPAdes pipeline for plasmid + detection. Default: false + +--spades_metaviral : Runs metaviralSPAdes pipeline for virus + detection. Default: false + +--spades_metaplasmid : Runs metaplasmidSPAdes pipeline for plasmid + detection in metagenomics datasets. Default: + false + +--spades_rnaviral : This flag enables virus assembly module + from RNA-Seq data. Default: false + +--spades_iontorrent : This flag is required for IonTorrent data. + Default: false + +--spades_only_assembler : Runs only the SPAdes assembler module ( + without read error correction). Default: + false + +--spades_careful : Tries to reduce the number of mismatches + and short indels in the assembly. Default: + false + +--spades_cov_cutoff : Coverage cutoff value (a positive float + number). Default: false + +--spades_k : List of k-mer sizes (must be odd and less + than 128). Default: false + +--spades_hmm : Directory with custom hmms that replace the + default ones (very rare). Default: false + +--serotypefinder_run : Run SerotypeFinder tool. Default: true + +--serotypefinder_x : Generate extended output files. Default: + true + +--serotypefinder_db : Path to SerotypeFinder databases. Default: / + hpc/db/serotypefinder/2.0.2 + +--serotypefinder_min_threshold : Minimum percent identity (in float) + required for calling a hit. Default: 0.85 + +--serotypefinder_min_cov : Minumum percent coverage (in float) + required for calling a hit. Default: 0.80 + +--seqsero2_run : Run SeqSero2 tool. Default: false + +--seqsero2_t : '1' for interleaved paired-end reads, '2' + for separated paired-end reads, '3' for + single reads, '4' for genome assembly, '5' + for nanopore reads (fasta/fastq). Default: + 4 + +--seqsero2_m : Which workflow to apply, 'a'(raw reads + allele micro-assembly), 'k'(raw reads and + genome assembly k-mer). Default: k + +--seqsero2_c : SeqSero2 will only output serotype + prediction without the directory containing + log files. Default: false + +--seqsero2_s : SeqSero2 will not output header in + SeqSero_result.tsv. Default: false + +--mlst_run : Run MLST tool. Default: true + +--mlst_minid : DNA %identity of full allelle to consider ' + similar' [~]. Default: 95 + +--mlst_mincov : DNA %cov to report partial allele at all [?]. + Default: 10 + +--mlst_minscore : Minumum score out of 100 to match a scheme. + Default: 50 + +--abricate_run : Run ABRicate tool. Default: true + +--abricate_minid : Minimum DNA %identity. Defaut: 90 + +--abricate_mincov : Minimum DNA %coverage. Defaut: 80 + +--abricate_datadir : ABRicate databases folder. Defaut: /hpc/db/ + abricate/1.0.1/db + +Help options : + +--help : Display this message. +```
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/subworkflows/process_fastq.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,144 @@ +// Include any necessary methods and modules +include { stopNow; validateParamsForFASTQ } from "${params.routines}" +include { GEN_SAMPLESHEET } from "${params.modules}${params.fs}gen_samplesheet${params.fs}main" +include { SAMPLESHEET_CHECK } from "${params.modules}${params.fs}samplesheet_check${params.fs}main" +include { CAT_FASTQ } from "${params.modules}${params.fs}cat${params.fs}fastq${params.fs}main" +include { SEQKIT_SEQ } from "${params.modules}${params.fs}seqkit${params.fs}seq${params.fs}main" + +// Validate 4 required workflow parameters if +// FASTQ files are the input for the +// entry point. +validateParamsForFASTQ() + +// Start the subworkflow +workflow PROCESS_FASTQ { + main: + versions = Channel.empty() + input_ch = Channel.empty() + reads = Channel.empty() + + def input = file( (params.input ?: params.metadata) ) + + if (params.input) { + def fastq_files = [] + + if (params.fq_suffix == null) { + stopNow("We need to know what suffix the FASTQ files ends with inside the\n" + + "directory. Please use the --fq_suffix option to indicate the file\n" + + "suffix by which the files are to be collected to run the pipeline on.") + } + + if (params.fq_strandedness == null) { + stopNow("We need to know if the FASTQ files inside the directory\n" + + "are sequenced using stranded or non-stranded sequencing. This is generally\n" + + "required if the sequencing experiment is RNA-SEQ. For almost all of the other\n" + + "cases, you can probably use the --fq_strandedness unstranded option to indicate\n" + + "that the reads are unstranded.") + } + + if (params.fq_filename_delim == null || params.fq_filename_delim_idx == null) { + stopNow("We need to know the delimiter of the filename of the FASTQ files.\n" + + "By default the filename delimiter is _ (underscore). This delimiter character\n" + + "is used to split and assign a group name. The group name can be controlled by\n" + + "using the --fq_filename_delim_idx option (1-based). For example, if the FASTQ\n" + + "filename is WT_REP1_001.fastq, then to create a group WT, use the following\n" + + "options: --fq_filename_delim _ --fq_filename_delim_idx 1") + } + + if (!input.exists()) { + stopNow("The input directory,\n${params.input}\ndoes not exist!") + } + + input.eachFileRecurse { + it.name.endsWith("${params.fq_suffix}") ? fastq_files << it : fastq_files << null + } + + if (fastq_files.findAll{ it != null }.size() == 0) { + stopNow("The input directory,\n${params.input}\nis empty! or does not " + + "have FASTQ files ending with the suffix: ${params.fq_suffix}") + } + + GEN_SAMPLESHEET( Channel.fromPath(params.input, type: 'dir') ) + GEN_SAMPLESHEET.out.csv.set{ input_ch } + versions.mix( GEN_SAMPLESHEET.out.versions ) + .set { versions } + } else if (params.metadata) { + if (!input.exists()) { + stopNow("The metadata CSV file,\n${params.metadata}\ndoes not exist!") + } + + if (input.size() <= 0) { + stopNow("The metadata CSV file,\n${params.metadata}\nis empty!") + } + + Channel.fromPath(params.metadata, type: 'file') + .set { input_ch } + } + + SAMPLESHEET_CHECK( input_ch ) + .csv + .splitCsv( header: true, sep: ',') + .map { create_fastq_channel(it) } + .groupTuple(by: [0]) + .branch { + meta, fastq -> + single : fastq.size() == 1 + return [ meta, fastq.flatten() ] + multiple : fastq.size() > 1 + return [ meta, fastq.flatten() ] + } + .set { reads } + + CAT_FASTQ( reads.multiple ) + .catted_reads + .mix( reads.single ) + .set { processed_reads } + + if (params.fq_filter_by_len.toInteger() > 0) { + SEQKIT_SEQ( processed_reads ) + .fastx + .set { processed_reads } + + versions.mix( SEQKIT_SEQ.out.versions.first().ifEmpty(null) ) + .set { versions } + } + + versions.mix( + SAMPLESHEET_CHECK.out.versions, + CAT_FASTQ.out.versions.first().ifEmpty(null) + ) + .set { versions } + + emit: + processed_reads + versions +} + +// Function to get list of [ meta, [ fq1, fq2 ] ] +def create_fastq_channel(LinkedHashMap row) { + + def meta = [:] + meta.id = row.sample + meta.single_end = row.single_end.toBoolean() + meta.strandedness = row.strandedness + meta.id = meta.id.split(params.fq_filename_delim)[0..params.fq_filename_delim_idx.toInteger() - 1] + .join(params.fq_filename_delim) + meta.id = (meta.id =~ /\./ ? meta.id.take(meta.id.indexOf('.')) : meta.id) + + def array = [] + + if (!file(row.fq1).exists()) { + stopNow("Please check input metadata CSV. The following Read 1 FASTQ file does not exist!" + + "\n${row.fq1}") + } + if (meta.single_end) { + array = [ meta, [ file(row.fq1) ] ] + } else { + if (!file(row.fq2).exists()) { + stopNow("Please check input metadata CSV. The following Read 2 FASTQ file does not exist!" + + "\n${row.fq2}") + } + array = [ meta, [ file(row.fq1), file(row.fq2) ] ] + } + return array +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/workflows/centriflaken.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,332 @@ +// Define any required imports for this specific workflow +import java.nio.file.Paths +import nextflow.file.FileHelper + +// Include any necessary methods +include { \ + summaryOfParams; stopNow; fastqEntryPointHelp; sendMail; \ + addPadding; wrapUpHelp } from "${params.routines}" +include { kraken2Help } from "${params.toolshelp}${params.fs}kraken2" +include { centrifugeHelp } from "${params.toolshelp}${params.fs}centrifuge" +include { flyeHelp } from "${params.toolshelp}${params.fs}flye" +include { serotypefinderHelp } from "${params.toolshelp}${params.fs}serotypefinder" +include { seqsero2Help } from "${params.toolshelp}${params.fs}seqsero2" +include { mlstHelp } from "${params.toolshelp}${params.fs}mlst" +include { abricateHelp } from "${params.toolshelp}${params.fs}abricate" + +// Exit if help requested before any subworkflows +if (params.help) { + log.info help() + exit 0 +} + +// Include any necessary modules and subworkflows +include { PROCESS_FASTQ } from "${params.subworkflows}${params.fs}process_fastq" +include { FASTQC } from "${params.modules}${params.fs}fastqc${params.fs}main" +include { CENTRIFUGE_CLASSIFY } from "${params.modules}${params.fs}centrifuge${params.fs}classify${params.fs}main" +include { CENTRIFUGE_PROCESS } from "${params.modules}${params.fs}centrifuge${params.fs}process${params.fs}main" +include { SEQKIT_GREP } from "${params.modules}${params.fs}seqkit${params.fs}grep${params.fs}main" +include { FLYE_ASSEMBLE } from "${params.modules}${params.fs}flye${params.fs}assemble${params.fs}main" +include { KRAKEN2_CLASSIFY } from "${params.modules}${params.fs}kraken2${params.fs}classify${params.fs}main" +include { KRAKEN2_EXTRACT_CONTIGS } from "${params.modules}${params.fs}kraken2${params.fs}extract_contigs${params.fs}main" +include { SEROTYPEFINDER } from "${params.modules}${params.fs}serotypefinder${params.fs}main" +include { SEQSERO2 } from "${params.modules}${params.fs}seqsero2${params.fs}main" +include { MLST } from "${params.modules}${params.fs}mlst${params.fs}main" +include { ABRICATE_RUN } from "${params.modules}${params.fs}abricate${params.fs}run${params.fs}main" +include { ABRICATE_SUMMARY } from "${params.modules}${params.fs}abricate${params.fs}summary${params.fs}main" +include { TABLE_SUMMARY } from "${params.modules}${params.fs}cat${params.fs}tables${params.fs}main" +include { MULTIQC } from "${params.modules}${params.fs}multiqc${params.fs}main" +include { DUMP_SOFTWARE_VERSIONS } from "${params.modules}${params.fs}custom${params.fs}dump_software_versions${params.fs}main" + + + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + INPUTS AND ANY CHECKS FOR THE CENTRIFLAKEN WORKFLOW +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +def kraken2_db_dir = file ( "${params.kraken2_db}" ) +def centrifuge_x = file ( "${params.centrifuge_x}" ) +def reads_platform = 0 +def abricate_dbs = [ 'ncbiamrplus', 'resfinder', 'megares', 'argannot' ] + +reads_platform += (params.flye_nano_raw ? 1 : 0) +reads_platform += (params.flye_nano_corr ? 1 : 0) +reads_platform += (params.flye_nano_hq ? 1 : 0) +reads_platform += (params.flye_pacbio_raw ? 1 : 0) +reads_platform += (params.flye_pacbio_corr ? 1 : 0) +reads_platform += (params.flye_pacbio_hifi ? 1 : 0) + +if (!kraken2_db_dir.exists() || !centrifuge_x.getParent().exists()) { + stopNow("Please check if the following absolute paths are valid:\n" + + "${params.kraken2_db}\n${params.centrifuge_x}\n" + + "Cannot proceed further!") +} + +if (reads_platform > 1 || reads_platform == 0) { + msg_0 = (reads_platform > 1 ? "only" : "at least") + stopNow("Please mention ${msg_0} one read platform for use with the flye assembler\n" + + "using any one of the following options:\n" + + "--flye_nano_raw\n--flye_nano_corr\n--flye_nano_hq\n" + + "--flye_pacbio_raw\n--flye_pacbio_corr\n--flye_pacbio_hifi") +} + +if (params.centrifuge_extract_bug != params.kraken2_extract_bug) { + stopNow("Please make sure that the bug to be extracted is same\n" + + "for both --centrifuge_extract_bug and --kraken2_extract_bug options.") +} + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + RUN THE CENTRIFLAKEN WORKFLOW +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +workflow CENTRIFLAKEN { + main: + ch_asm_filtered_contigs = Channel.empty() + ch_mqc_custom_tbl = Channel.empty() + + log.info summaryOfParams() + + PROCESS_FASTQ() + .processed_reads + .map { + meta, fastq -> + meta.centrifuge_x = params.centrifuge_x + meta.kraken2_db = params.kraken2_db + [meta, fastq] + } + .set { ch_processed_reads } + + PROCESS_FASTQ + .out + .versions + .set { software_versions } + + FASTQC ( ch_processed_reads ) + + CENTRIFUGE_CLASSIFY ( ch_processed_reads ) + + CENTRIFUGE_PROCESS ( + CENTRIFUGE_CLASSIFY.out.report + .join( CENTRIFUGE_CLASSIFY.out.output ) + ) + + ch_processed_reads.join ( CENTRIFUGE_PROCESS.out.extracted ) + .set { ch_centrifuge_extracted } + + SEQKIT_GREP ( ch_centrifuge_extracted ) + + FLYE_ASSEMBLE ( SEQKIT_GREP.out.fastx ) + + FLYE_ASSEMBLE + .out + .assembly + .set { ch_flye_assembly } + + ch_flye_assembly + .map { + meta, fastq -> + meta.is_assembly = true + [meta, fastq] + } + .set { ch_flye_assembly } + + ch_flye_assembly.ifEmpty { [ false, false ] } + + KRAKEN2_CLASSIFY ( ch_flye_assembly ) + + KRAKEN2_EXTRACT_CONTIGS ( + ch_flye_assembly + .join( KRAKEN2_CLASSIFY.out.kraken_output ), + params.kraken2_extract_bug + ) + + KRAKEN2_EXTRACT_CONTIGS + .out + .asm_filtered_contigs + .map { + meta, fastq -> + meta.organism = params.kraken2_extract_bug.split(/\s+/)[0].capitalize() + meta.serotypefinder_db = params.serotypefinder_db + [meta, fastq] + } + .set { ch_asm_filtered_contigs } + + SEROTYPEFINDER ( ch_asm_filtered_contigs ) + + SEQSERO2 ( ch_asm_filtered_contigs ) + + MLST ( ch_asm_filtered_contigs ) + + ABRICATE_RUN ( + ch_asm_filtered_contigs, + abricate_dbs + ) + + ABRICATE_RUN + .out + .abricated + .map { meta, abres -> [ abricate_dbs, abres ] } + .groupTuple(by: [0]) + .map { it -> tuple ( it[0], it[1].flatten() ) } + .set { ch_abricated } + + ABRICATE_SUMMARY ( ch_abricated ) + + // ABRICATE_SUMMARY.out.ecoli_vf.set { ch_abricate_summary_ecoli_vf } + // ch_abricate_summary_ecoli_vf.ifEmpty { [ false, false ] } + + CENTRIFUGE_CLASSIFY.out.kreport + .map { meta, kreport -> [ kreport ] } + .flatten() + .concat ( + KRAKEN2_CLASSIFY.out.kraken_report + .map { meta, kreport -> [ kreport ] } + .flatten(), + FASTQC.out.zip + .map { meta, zip -> [ zip ] } + .flatten() + ) + .set { ch_mqc_classify } + + if (params.serotypefinder_run) { + SEROTYPEFINDER + .out + .serotyped + .map { meta, tsv -> [ 'serotypefinder', tsv ] } + .groupTuple(by: [0]) + .map { it -> tuple ( it[0], it[1].flatten() ) } + .set { ch_mqc_custom_tbl } + } else if (params.seqsero2_run) { + SEQSERO2 + .out + .serotyped + .map { meta, tsv -> [ 'seqsero2', tsv ] } + .groupTuple(by: [0]) + .map { it -> tuple ( it[0], it[1].flatten() ) } + .set { ch_mqc_custom_tbl } + } + + ch_mqc_custom_tbl + .concat ( + ABRICATE_SUMMARY.out.ncbiamrplus.map{ it -> tuple ( it[0], it[1] )}, + ABRICATE_SUMMARY.out.resfinder.map{ it -> tuple ( it[0], it[1] )}, + ABRICATE_SUMMARY.out.megares.map{ it -> tuple ( it[0], it[1] )}, + ABRICATE_SUMMARY.out.argannot.map{ it -> tuple ( it[0], it[1] )}, + ) + .groupTuple(by: [0]) + .map { it -> [ it[0], it[1].flatten() ]} + .set { ch_mqc_custom_tbl } + + TABLE_SUMMARY ( ch_mqc_custom_tbl ) + + DUMP_SOFTWARE_VERSIONS ( + software_versions + .mix ( + FASTQC.out.versions, + CENTRIFUGE_CLASSIFY.out.versions, + CENTRIFUGE_PROCESS.out.versions, + SEQKIT_GREP.out.versions, + FLYE_ASSEMBLE.out.versions.ifEmpty(null), + KRAKEN2_CLASSIFY.out.versions.ifEmpty(null), + KRAKEN2_EXTRACT_CONTIGS.out.versions.ifEmpty(null), + SEROTYPEFINDER.out.versions.ifEmpty(null), + SEQSERO2.out.versions.ifEmpty(null), + MLST.out.versions.ifEmpty(null), + ABRICATE_RUN.out.versions.ifEmpty(null), + ABRICATE_SUMMARY.out.versions.ifEmpty(null), + TABLE_SUMMARY.out.versions.ifEmpty(null) + ) + .unique() + .collectFile(name: 'collected_versions.yml') + ) + + DUMP_SOFTWARE_VERSIONS + .out + .mqc_yml + .concat ( + ch_mqc_classify, + TABLE_SUMMARY.out.mqc_yml + ) + .collect() + .set { ch_multiqc } + + MULTIQC ( ch_multiqc ) +} + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + ON COMPLETE, SHOW GORY DETAILS OF ALL PARAMS WHICH WILL BE HELPFUL TO DEBUG +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +workflow.onComplete { + if (workflow.success) { + // CREATE APPROPRIATE DIRECTORIES AND MOVE AS REQUESTED BY STAKEHOLDER(S) + // + // Nextflow's .moveTo will error out if directories contain files and it + // would be complex to include logic to skip directories + // + def final_intermediate_dir = "${params.output}${params.fs}${params.pipeline}-steps" + def final_results_dir = "${params.output}${params.fs}${params.pipeline}-results" + def kraken2_ext_contigs = file( "${final_intermediate_dir}${params.fs}kraken2_extract_contigs", type: 'dir' ) + def final_intermediate = file( final_intermediate_dir, type: 'dir' ) + def final_results = file( final_results_dir, type: 'dir' ) + def pipeline_output = file( params.output, type: 'dir' ) + + if ( !final_intermediate.exists() ) { + final_intermediate.mkdirs() + + FileHelper.visitFiles(Paths.get("${params.output}"), '*') { + if ( !(it.name ==~ /^(${params.cfsanpipename}|multiqc|\.nextflow|${workflow.workDir.name}|${params.pipeline}).*/) ) { + FileHelper.movePath( + it, Paths.get( "${final_intermediate_dir}${params.fs}${it.name}" ) + ) + } + } + } + + if ( kraken2_ext_contigs.exists() && !final_results.exists() ) { + final_results.mkdirs() + + FileHelper.movePath( + Paths.get( "${final_intermediate_dir}${params.fs}kraken2_extract_contigs" ), + Paths.get( "${final_results_dir}${params.fs}kraken2_extract_contigs" ) + ) + } + + sendMail() + } +} + +workflow.onError { + sendMail() +} + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + HELPER METHODS FOR CENTRIFLAKEN WORKFLOW +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +def help() { + + Map helptext = [:] + + helptext.putAll ( + fastqEntryPointHelp() + + kraken2Help(params).text + + centrifugeHelp(params).text + + flyeHelp(params).text + + serotypefinderHelp(params).text + + seqsero2Help(params).text + + mlstHelp(params).text + + abricateHelp(params).text + + wrapUpHelp() + ) + + return addPadding(helptext) +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/workflows/centriflaken_hy.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,375 @@ +// Define any required imports for this specific workflow +import java.nio.file.Paths +import nextflow.file.FileHelper + +// Include any necessary methods +include { \ + summaryOfParams; stopNow; fastqEntryPointHelp; sendMail; \ + addPadding; wrapUpHelp } from "${params.routines}" +include { seqkitrmdupHelp } from "${params.toolshelp}${params.fs}seqkitrmdup" +include { kraken2Help } from "${params.toolshelp}${params.fs}kraken2" +include { centrifugeHelp } from "${params.toolshelp}${params.fs}centrifuge" +include { megahitHelp } from "${params.toolshelp}${params.fs}megahit" +include { spadesHelp } from "${params.toolshelp}${params.fs}spades" +include { serotypefinderHelp } from "${params.toolshelp}${params.fs}serotypefinder" +include { seqsero2Help } from "${params.toolshelp}${params.fs}seqsero2" +include { mlstHelp } from "${params.toolshelp}${params.fs}mlst" +include { abricateHelp } from "${params.toolshelp}${params.fs}abricate" + +// Exit if help requested before any subworkflows +if (params.help) { + log.info help() + exit 0 +} + +// Include any necessary modules and subworkflows +include { PROCESS_FASTQ } from "${params.subworkflows}${params.fs}process_fastq" +include { FASTQC } from "${params.modules}${params.fs}fastqc${params.fs}main" +include { SEQKIT_RMDUP } from "${params.modules}${params.fs}seqkit${params.fs}rmdup${params.fs}main" +include { CENTRIFUGE_CLASSIFY } from "${params.modules}${params.fs}centrifuge${params.fs}classify${params.fs}main" +include { CENTRIFUGE_PROCESS } from "${params.modules}${params.fs}centrifuge${params.fs}process${params.fs}main" +include { SEQKIT_GREP } from "${params.modules}${params.fs}seqkit${params.fs}grep${params.fs}main" +include { MEGAHIT_ASSEMBLE } from "${params.modules}${params.fs}megahit${params.fs}assemble${params.fs}main" +include { SPADES_ASSEMBLE } from "${params.modules}${params.fs}spades${params.fs}assemble${params.fs}main" +include { KRAKEN2_CLASSIFY } from "${params.modules}${params.fs}kraken2${params.fs}classify${params.fs}main" +include { KRAKEN2_EXTRACT_CONTIGS } from "${params.modules}${params.fs}kraken2${params.fs}extract_contigs${params.fs}main" +include { SEROTYPEFINDER } from "${params.modules}${params.fs}serotypefinder${params.fs}main" +include { SEQSERO2 } from "${params.modules}${params.fs}seqsero2${params.fs}main" +include { MLST } from "${params.modules}${params.fs}mlst${params.fs}main" +include { ABRICATE_RUN } from "${params.modules}${params.fs}abricate${params.fs}run${params.fs}main" +include { ABRICATE_SUMMARY } from "${params.modules}${params.fs}abricate${params.fs}summary${params.fs}main" +include { TABLE_SUMMARY } from "${params.modules}${params.fs}cat${params.fs}tables${params.fs}main" +include { MULTIQC } from "${params.modules}${params.fs}multiqc${params.fs}main" +include { DUMP_SOFTWARE_VERSIONS } from "${params.modules}${params.fs}custom${params.fs}dump_software_versions${params.fs}main" + + + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + INPUTS AND ANY CHECKS FOR THE CENTRIFLAKEN-HY WORKFLOW +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +def kraken2_db_dir = file ( "${params.kraken2_db}" ) +def centrifuge_x = file ( "${params.centrifuge_x}" ) +def spades_custom_hmm = (params.spades_hmm ? file ( "${params.spades_hmm}" ) : false) +def reads_platform = 0 +def abricate_dbs = [ 'ncbiamrplus', 'resfinder', 'megares', 'argannot' ] + +reads_platform += (params.input ? 1 : 0) + +if (!kraken2_db_dir.exists() || !centrifuge_x.getParent().exists()) { + stopNow("Please check if the following absolute paths are valid:\n" + + "${params.kraken2_db}\n${params.centrifuge_x}\n" + + "Cannot proceed further!") +} + +if (spades_custom_hmm && !spades_custom_hmm.exists()) { + stopNow("Please check if the following SPAdes' custom HMM directory\n" + + "path is valid:\n${params.spades_hmm}\nCannot proceed further!") +} + +if (reads_platform < 1 || reads_platform == 0) { + stopNow("Please mention at least one absolute path to input folder which contains\n" + + "FASTQ files sequenced using the --input option.\n" + + "Ex: --input (Illumina or Generic short reads in FASTQ format)") +} + +if (params.centrifuge_extract_bug != params.kraken2_extract_bug) { + stopNow("Please make sure that the bug to be extracted is same\n" + + "for both --centrifuge_extract_bug and --kraken2_extract_bug options.") +} + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + RUN THE CENTRIFLAKEN-HY WORKFLOW +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +workflow CENTRIFLAKEN_HY { + main: + ch_asm_filtered_contigs = Channel.empty() + ch_mqc_custom_tbl = Channel.empty() + ch_dummy = Channel.fromPath("${params.dummyfile}") + ch_dummy2 = Channel.fromPath("${params.dummyfile2}") + + log.info summaryOfParams() + + PROCESS_FASTQ() + .processed_reads + .map { + meta, fastq -> + meta.centrifuge_x = params.centrifuge_x + meta.kraken2_db = params.kraken2_db + [meta, fastq] + } + .set { ch_processed_reads } + + PROCESS_FASTQ + .out + .versions + .set { software_versions } + + FASTQC ( ch_processed_reads ) + + if (params.seqkit_rmdup_run) { + SEQKIT_RMDUP ( ch_processed_reads ) + + SEQKIT_RMDUP + .out + .fastx + .set { ch_processed_reads } + + software_versions + .mix ( SEQKIT_RMDUP.out.versions.ifEmpty(null) ) + .set { software_versions } + } + + CENTRIFUGE_CLASSIFY ( ch_processed_reads ) + + CENTRIFUGE_PROCESS ( + CENTRIFUGE_CLASSIFY.out.report + .join( CENTRIFUGE_CLASSIFY.out.output ) + ) + + ch_processed_reads.join ( CENTRIFUGE_PROCESS.out.extracted ) + .set { ch_centrifuge_extracted } + + SEQKIT_GREP ( ch_centrifuge_extracted ) + + // As of 06/02/2022, with the upcoming newer versions of NextFlow, we will be able to do + // allowNull: true for both input and output, but until then, we have to use dummy files. + // and work arounds. + // https://github.com/nextflow-io/nextflow/pull/2893 + if (params.spades_run) { + SPADES_ASSEMBLE ( + SEQKIT_GREP.out.fastx + .combine(ch_dummy) + .combine(ch_dummy2) + ) + + SPADES_ASSEMBLE + .out + .assembly + .set { ch_assembly } + + software_versions + .mix ( SPADES_ASSEMBLE.out.versions.ifEmpty(null) ) + .set { software_versions } + } else if (params.megahit_run) { + MEGAHIT_ASSEMBLE ( + SEQKIT_GREP.out.fastx + ) + + MEGAHIT_ASSEMBLE + .out + .assembly + .set { ch_assembly } + + software_versions + .mix ( MEGAHIT_ASSEMBLE.out.versions.ifEmpty(null) ) + .set { software_versions } + } + + ch_assembly + .map { + meta, fastq -> + meta.is_assembly = true + [meta, fastq] + } + .set { ch_assembly } + + ch_assembly.ifEmpty { [ false, false ] } + + KRAKEN2_CLASSIFY ( ch_assembly ) + + KRAKEN2_EXTRACT_CONTIGS ( + ch_assembly + .join( KRAKEN2_CLASSIFY.out.kraken_output ), + params.kraken2_extract_bug + ) + + KRAKEN2_EXTRACT_CONTIGS + .out + .asm_filtered_contigs + .map { + meta, fastq -> + meta.organism = params.kraken2_extract_bug.split(/\s+/)[0].capitalize() + meta.serotypefinder_db = params.serotypefinder_db + [meta, fastq] + } + .set { ch_asm_filtered_contigs } + + SEROTYPEFINDER ( ch_asm_filtered_contigs ) + + SEQSERO2 ( ch_asm_filtered_contigs ) + + MLST ( ch_asm_filtered_contigs ) + + ABRICATE_RUN ( + ch_asm_filtered_contigs, + abricate_dbs + ) + + ABRICATE_RUN + .out + .abricated + .map { meta, abres -> [ abricate_dbs, abres ] } + .groupTuple(by: [0]) + .map { it -> tuple ( it[0], it[1].flatten() ) } + .set { ch_abricated } + + ABRICATE_SUMMARY ( ch_abricated ) + + CENTRIFUGE_CLASSIFY.out.kreport + .map { meta, kreport -> [ kreport ] } + .flatten() + .concat ( + KRAKEN2_CLASSIFY.out.kraken_report + .map { meta, kreport -> [ kreport ] } + .flatten(), + FASTQC.out.zip + .map { meta, zip -> [ zip ] } + .flatten() + ) + .set { ch_mqc_classify } + + if (params.serotypefinder_run) { + SEROTYPEFINDER + .out + .serotyped + .map { meta, tsv -> [ 'serotypefinder', tsv ] } + .groupTuple(by: [0]) + .map { it -> tuple ( it[0], it[1].flatten() ) } + .set { ch_mqc_custom_tbl } + } else if (params.seqsero2_run) { + SEQSERO2 + .out + .serotyped + .map { meta, tsv -> [ 'seqsero2', tsv ] } + .groupTuple(by: [0]) + .map { it -> tuple ( it[0], it[1].flatten() ) } + .set { ch_mqc_custom_tbl } + } + + ch_mqc_custom_tbl + .concat ( + ABRICATE_SUMMARY.out.ncbiamrplus.map{ it -> tuple ( it[0], it[1] )}, + ABRICATE_SUMMARY.out.resfinder.map{ it -> tuple ( it[0], it[1] )}, + ABRICATE_SUMMARY.out.megares.map{ it -> tuple ( it[0], it[1] )}, + ABRICATE_SUMMARY.out.argannot.map{ it -> tuple ( it[0], it[1] )}, + ) + .groupTuple(by: [0]) + .map { it -> [ it[0], it[1].flatten() ]} + .set { ch_mqc_custom_tbl } + + TABLE_SUMMARY ( ch_mqc_custom_tbl ) + + DUMP_SOFTWARE_VERSIONS ( + software_versions + .mix ( + FASTQC.out.versions, + CENTRIFUGE_CLASSIFY.out.versions, + CENTRIFUGE_PROCESS.out.versions, + SEQKIT_GREP.out.versions, + KRAKEN2_CLASSIFY.out.versions.ifEmpty(null), + KRAKEN2_EXTRACT_CONTIGS.out.versions.ifEmpty(null), + SEROTYPEFINDER.out.versions.ifEmpty(null), + SEQSERO2.out.versions.ifEmpty(null), + MLST.out.versions.ifEmpty(null), + ABRICATE_RUN.out.versions.ifEmpty(null), + ABRICATE_SUMMARY.out.versions.ifEmpty(null), + TABLE_SUMMARY.out.versions.ifEmpty(null) + ) + .unique() + .collectFile(name: 'collected_versions.yml') + ) + + DUMP_SOFTWARE_VERSIONS + .out + .mqc_yml + .concat ( + ch_mqc_classify, + TABLE_SUMMARY.out.mqc_yml + ) + .collect() + .set { ch_multiqc } + + MULTIQC ( ch_multiqc ) +} + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + ON COMPLETE, SHOW GORY DETAILS OF ALL PARAMS WHICH WILL BE HELPFUL TO DEBUG +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +workflow.onComplete { + if (workflow.success) { + // CREATE APPROPRIATE DIRECTORIES AND MOVE AS REQUESTED BY STAKEHOLDER(S) + // + // Nextflow's .moveTo will error out if directories contain files and it + // would be complex to include logic to skip directories + // + def final_intermediate_dir = "${params.output}${params.fs}${params.pipeline}-steps" + def final_results_dir = "${params.output}${params.fs}${params.pipeline}-results" + def kraken2_ext_contigs = file( "${final_intermediate_dir}${params.fs}kraken2_extract_contigs", type: 'dir' ) + def final_intermediate = file( final_intermediate_dir, type: 'dir' ) + def final_results = file( final_results_dir, type: 'dir' ) + def pipeline_output = file( params.output, type: 'dir' ) + + if ( !final_intermediate.exists() ) { + final_intermediate.mkdirs() + + FileHelper.visitFiles(Paths.get("${params.output}"), '*') { + if ( !(it.name ==~ /^(${params.cfsanpipename}|multiqc|\.nextflow|${workflow.workDir.name}|${params.pipeline}).*/) ) { + FileHelper.movePath( + it, Paths.get( "${final_intermediate_dir}${params.fs}${it.name}" ) + ) + } + } + } + + if ( kraken2_ext_contigs.exists() && !final_results.exists() ) { + final_results.mkdirs() + + FileHelper.movePath( + Paths.get( "${final_intermediate_dir}${params.fs}kraken2_extract_contigs" ), + Paths.get( "${final_results_dir}${params.fs}kraken2_extract_contigs" ) + ) + } + + sendMail() + } +} + +workflow.onError { + sendMail() +} + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + HELPER METHODS FOR CENTRIFLAKEN-HY WORKFLOW +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +def help() { + + Map helptext = [:] + + helptext.putAll ( + fastqEntryPointHelp() + + seqkitrmdupHelp(params).text + + kraken2Help(params).text + + centrifugeHelp(params).text + + megahitHelp(params).text + + spadesHelp(params).text + + serotypefinderHelp(params).text + + seqsero2Help(params).text + + mlstHelp(params).text + + abricateHelp(params).text + + wrapUpHelp() + ) + + return addPadding(helptext) +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/workflows/conf/centriflaken.config Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,58 @@ +params { + workflow_built_by = 'Kranti.Konganti@fda.hhs.gov' + workflow_version = '0.2.2' + centrifuge_x = '/server/galaxy/tool-data/centriflaken-dbs/centrifuge/2022-04-12/ab' + centrifuge_extract_bug = 'Escherichia coli' + centrifuge_save_aligned = false + centrifuge_save_unaligned = false + centrifuge_out_fmt_sam = false + centrifuge_ignore_quals = false + kraken2_db = '/server/galaxy/tool-data/centriflaken-dbs/kraken2/standard-210914' + kraken2_confidence = '0.0' + kraken2_quick = false + kraken2_use_mpa_style = false + kraken2_minimum_base_quality = '0' + kraken2_report_zero_counts = false + kraken2_report_minimizer_data = false + kraken2_use_names = true + kraken2_extract_bug = params.centrifuge_extract_bug + flye_pacbio_raw = false + flye_pacbio_corr = false + flye_pacbio_hifi = false + flye_nano_raw = true + flye_nano_corr = false + flye_nano_hq = false + flye_genome_size = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? '5m' : '5.5m') + flye_polish_iter = false + flye_min_overlap = false + flye_scaffold = false + flye_meta = true + ectyper_run = false + ectyper_perc_opid = 90 + ectyper_perc_hpid = 95 + ectyper_perc_opcov = 95 + ectyper_perc_hpcov = 50 + serotypefinder_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? false : true) + serotypefinder_db = '/server/galaxy/tool-data/centriflaken-dbs/serotypefinder/2.0.2' + serotypefinder_min_cov = 0.80 + serotypefinder_min_threshold = 0.85 + serotypefinder_x = true + seqsero2_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? true : false) + seqsero2_t = 4 + seqsero2_m = 'k' + seqsero2_c = false + seqsero2_s = false + mlst_run = true + mlst_minid = 95 + mlst_mincov = 10 + mlst_minscore = 50 + amrfinderplus_run = false + amrfinderplus_db = '/server/galaxy/tool-data/centriflaken-dbs/amrfinderplus/3.10.24/latest' + amrfinderplus_genes = true + abricate_run = true + abricate_datadir = '/server/galaxy/tool-data/centriflaken-dbs/abricate/1.0.1/db' + abricate_minid = 90 + abricate_mincov = 80 + abricate_summary_run = true + seqkit_grep_on = false +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/workflows/conf/centriflaken_hy.config Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,89 @@ +params { + workflow_built_by = 'Kranti.Konganti@fda.hhs.gov' + workflow_version = '0.4.1' + seqkit_rmdup_run = false + seqkit_rmdup_n = false + seqkit_rmdup_s = true + seqkit_rmdup_d = false + seqkit_rmdup_D = false + seqkit_rmdup_P = false + seqkit_rmdup_i = false + centrifuge_x = '/server/galaxy/tool-data/centriflaken-dbs/centrifuge/2022-04-12/ab' + centrifuge_extract_bug = 'Escherichia coli' + centrifuge_save_aligned = false + centrifuge_save_unaligned = false + centrifuge_out_fmt_sam = false + centrifuge_ignore_quals = false + kraken2_db = '/server/galaxy/tool-data/centriflaken-dbs/kraken2/standard-210914' + kraken2_confidence = '0.0' + kraken2_quick = false + kraken2_use_mpa_style = false + kraken2_minimum_base_quality = '0' + kraken2_report_zero_counts = false + kraken2_report_minimizer_data = false + kraken2_use_names = true + kraken2_extract_bug = params.centrifuge_extract_bug + megahit_run = true + megahit_min_count = false + megahit_k_list = false + megahit_no_mercy = false + megahit_bubble_level = false + megahit_merge_level = false + megahit_prune_level = false + megahit_prune_depth = false + megahit_low_local_ratio = false + megahit_max_tip_len = false + megahit_no_local = false + megahit_kmin_1pass = false + megahit_preset = 'meta-sensitive' + megahit_mem_flag = 2 + megahit_min_contig_len = false + spades_run = false + spades_isolate = false + spades_sc = false + spades_meta = true + spades_bio = false + spades_corona = false + spades_rna = false + spades_plasmid = false + spades_metaviral = false + spades_metaplasmid = false + spades_rnaviral = false + spades_iontorrent = false + spades_only_assembler = false + spades_careful = false + spades_cov_cutoff = false + spades_k = false + spades_hmm = false + ectyper_run = false + ectyper_perc_opid = 90 + ectyper_perc_hpid = 95 + ectyper_perc_opcov = 95 + ectyper_perc_hpcov = 50 + serotypefinder_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? false : true) + serotypefinder_db = '/server/galaxy/tool-data/centriflaken-dbs/serotypefinder/2.0.2' + serotypefinder_min_cov = 0.80 + serotypefinder_min_threshold = 0.85 + serotypefinder_x = true + seqsero2_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? true : false) + seqsero2_t = 4 + seqsero2_m = 'k' + seqsero2_c = false + seqsero2_s = false + mlst_run = true + mlst_minid = 95 + mlst_mincov = 10 + mlst_minscore = 50 + amrfinderplus_run = false + amrfinderplus_db = '/server/galaxy/tool-data/centriflaken-dbs/amrfinderplus/3.10.24/latest' + amrfinderplus_genes = true + abricate_run = true + abricate_datadir = '/server/galaxy/tool-data/centriflaken-dbs/abricate/1.0.1/db' + abricate_minid = 90 + abricate_mincov = 80 + abricate_summary_run = true + seqkit_grep_on = false + fq_filter_by_len = 75 + fq_suffix = '_R1_001.fastq.gz' + fq2_suffix = '_R2_001.fastq.gz' +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/workflows/conf/nanofactory.config Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,21 @@ +params { + workflow_author = "Rodney.Engelbach@fda.hhs.gov" + workflow_version = "0.4.1" + sample_sheet = "" + global_settings = "" + log_file = "" + log_level = "info" + mode = "" + verbose = false + disable_project_setup = false + setup_purge_existing = false + setup_fix_existing = true + setup_nocopy = false + setup_runtype = "" + guppy_threads = 4 + guppy_config = "" + merge_overwrite = false + mail_group = "stakeholders" + help = false + enable_module = "'nanofactory/current'" +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/workflows/conf/process/centriflaken.process.config Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,111 @@ +process { + withName: 'SEQKIT_SEQ' { + ext.args = [ + params.fq_filter_by_len ? "-m ${params.fq_filter_by_len}" : '' + ].join(' ').trim() + } + + if (params.seqkit_grep_on) { + withName: 'SEQKIT_GREP' { + ext.args = addParamsToSummary( + loadThisFunction("${params.toolshelp}${params.fs}seqkitgrep.nf").seqkitgrepHelp(params).helpparams + ) + } + } + + withName: 'CENTRIFUGE_CLASSIFY' { + ext.args = addParamsToSummary( + loadThisFunction("${params.toolshelp}${params.fs}centrifuge.nf").centrifugeHelp(params).helpparams + ) + } + + withName: 'KRAKEN2_CLASSIFY' { + ext.args = addParamsToSummary( + loadThisFunction("${params.toolshelp}${params.fs}kraken2.nf").kraken2Help(params).helpparams + ) + } + + withName: 'FLYE_ASSEMBLE' { + errorStrategy = 'ignore' + ext.args = addParamsToSummary( + loadThisFunction("${params.toolshelp}${params.fs}flye.nf").flyeHelp(params).helpparams + ) + } + + if (params.ectyper_run) { + withName: 'ECTYPER' { + ext.when = params.ectyper_run + ext.args = addParamsToSummary( + loadThisFunction("${params.toolshelp}${params.fs}ectyper.nf").ectyperHelp(params).helpparams + ) + } + } + + withName: 'SEROTYPEFINDER' { + ext.when = params.serotypefinder_run + ext.args = addParamsToSummary( + loadThisFunction("${params.toolshelp}${params.fs}serotypefinder.nf").serotypefinderHelp(params).helpparams + ) + } + + withName: 'SEQSERO2' { + ext.when = params.seqsero2_run + ext.args = addParamsToSummary( + loadThisFunction("${params.toolshelp}${params.fs}seqsero2.nf").seqsero2Help(params).helpparams + ) + } + + withName: 'MLST' { + ext.when = params.mlst_run + ext.args = addParamsToSummary( + loadThisFunction("${params.toolshelp}${params.fs}mlst.nf").mlstHelp(params).helpparams + ) + } + + if (params.amrfinderplus_run) { + withName: 'AMRFINDERPLUS_RUN' { + ext.when = params.amrfinderplus_run + ext.args = addParamsToSummary( + loadThisFunction("${params.toolshelp}${params.fs}amrfinderplus.nf").amrfinderplusHelp(params).helpparams + ) + } + } + + withName: 'ABRICATE_RUN' { + ext.when = params.abricate_run + ext.args = addParamsToSummary( + loadThisFunction("${params.toolshelp}${params.fs}abricate.nf").abricateHelp(params).helpparams + ) + } + + withName: 'ABRICATE_SUMMARY' { + ext.when = params.abricate_summary_run + } +} + +// Method to instantiate a new function parser +// Need to refactor using ScriptParser... another day +def loadThisFunction (func_file) { + GroovyShell grvy_sh = new GroovyShell() + def func = grvy_sh.parse(new File ( func_file ) ) + return func +} + +// Method to add relevant final parameters to summary log +def addParamsToSummary(Map params_to_add = [:]) { + + if (!params_to_add.isEmpty()) { + def not_null_params_to_add = params_to_add.findAll { + it.value.clivalue != null && + it.value.clivalue != '[:]' && + it.value.clivalue != '' + } + + params.logtheseparams += not_null_params_to_add.keySet().toList() + + return not_null_params_to_add.collect { + "${it.value.cliflag} ${it.value.clivalue.toString().replaceAll(/(?:^\s+|\s+$)/, '')}" + }.join(' ').trim() + } + return 1 +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/workflows/conf/process/centriflaken_hy.process.config Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,129 @@ +process { + withName: 'SEQKIT_SEQ' { + ext.args = [ + params.fq_filter_by_len ? "-m ${params.fq_filter_by_len}" : '' + ].join(' ').trim() + } + + if (params.seqkit_rmdup_run) { + withName: 'SEQKIT_RMDUP' { + ext.when = params.seqkit_rmdup_run + ext.args = addParamsToSummary( + loadThisFunction("${params.toolshelp}${params.fs}seqkitrmdup.nf").seqkitrmdupHelp(params).helpparams + ) + } + } + + if (params.seqkit_grep_on) { + withName: 'SEQKIT_GREP' { + ext.args = addParamsToSummary( + loadThisFunction("${params.toolshelp}${params.fs}seqkitgrep.nf").seqkitgrepHelp(params).helpparams + ) + } + } + + withName: 'CENTRIFUGE_CLASSIFY' { + ext.args = addParamsToSummary( + loadThisFunction("${params.toolshelp}${params.fs}centrifuge.nf").centrifugeHelp(params).helpparams + ) + } + + withName: 'KRAKEN2_CLASSIFY' { + ext.args = addParamsToSummary( + loadThisFunction("${params.toolshelp}${params.fs}kraken2.nf").kraken2Help(params).helpparams + ) + } + + withName: 'MEGAHIT_ASSEMBLE' { + ext.when = params.megahit_run + errorStrategy = 'ignore' + ext.args = addParamsToSummary( + loadThisFunction("${params.toolshelp}${params.fs}megahit.nf").megahitHelp(params).helpparams + ) + } + + withName: 'SPADES_ASSEMBLE' { + ext.when = params.spades_run + errorStrategy = 'ignore' + ext.args = addParamsToSummary( + loadThisFunction("${params.toolshelp}${params.fs}spades.nf").spadesHelp(params).helpparams + ) + } + + if (params.ectyper_run) { + withName: 'ECTYPER' { + ext.when = params.ectyper_run + ext.args = addParamsToSummary( + loadThisFunction("${params.toolshelp}${params.fs}ectyper.nf").ectyperHelp(params).helpparams + ) + } + } + + withName: 'SEROTYPEFINDER' { + ext.when = params.serotypefinder_run + ext.args = addParamsToSummary( + loadThisFunction("${params.toolshelp}${params.fs}serotypefinder.nf").serotypefinderHelp(params).helpparams + ) + } + + withName: 'SEQSERO2' { + ext.when = params.seqsero2_run + ext.args = addParamsToSummary( + loadThisFunction("${params.toolshelp}${params.fs}seqsero2.nf").seqsero2Help(params).helpparams + ) + } + + withName: 'MLST' { + ext.when = params.mlst_run + ext.args = addParamsToSummary( + loadThisFunction("${params.toolshelp}${params.fs}mlst.nf").mlstHelp(params).helpparams + ) + } + + if (params.amrfinderplus_run) { + withName: 'AMRFINDERPLUS_RUN' { + ext.when = params.amrfinderplus_run + ext.args = addParamsToSummary( + loadThisFunction("${params.toolshelp}${params.fs}amrfinderplus.nf").amrfinderplusHelp(params).helpparams + ) + } + } + + withName: 'ABRICATE_RUN' { + ext.when = params.abricate_run + ext.args = addParamsToSummary( + loadThisFunction("${params.toolshelp}${params.fs}abricate.nf").abricateHelp(params).helpparams + ) + } + + withName: 'ABRICATE_SUMMARY' { + ext.when = params.abricate_summary_run + } +} + +// Method to instantiate a new function parser +// Need to refactor using ScriptParser... another day +def loadThisFunction (func_file) { + GroovyShell grvy_sh = new GroovyShell() + def func = grvy_sh.parse(new File ( func_file ) ) + return func +} + +// Method to add relevant final parameters to summary log +def addParamsToSummary(Map params_to_add = [:]) { + + if (!params_to_add.isEmpty()) { + def not_null_params_to_add = params_to_add.findAll { + it.value.clivalue != null && + it.value.clivalue != '[:]' && + it.value.clivalue != '' + } + + params.logtheseparams += not_null_params_to_add.keySet().toList() + + return not_null_params_to_add.collect { + "${it.value.cliflag} ${it.value.clivalue.toString().replaceAll(/(?:^\s+|\s+$)/, '')}" + }.join(' ').trim() + } + return 1 +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/workflows/conf/process/spades_only.process.config Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,34 @@ +process { + withName: 'SPADES_ASSEMBLE' { + ext.args = addParamsToSummary( + loadThisFunction("${params.toolshelp}${params.fs}spades.nf").spadesHelp(params).helpparams + ) + } +} + +// Method to instantiate a new function parser +// Need to refactor using ScriptParser... another day +def loadThisFunction (func_file) { + GroovyShell grvy_sh = new GroovyShell() + def func = grvy_sh.parse(new File ( func_file ) ) + return func +} + +// Method to add relevant final parameters to summary log +def addParamsToSummary(Map params_to_add = [:]) { + + if (!params_to_add.isEmpty()) { + def not_null_params_to_add = params_to_add.findAll { + it.value.clivalue != null && + it.value.clivalue != '[:]' && + it.value.clivalue != '' + } + + params.logtheseparams += not_null_params_to_add.keySet().toList() + + return not_null_params_to_add.collect { + "${it.value.cliflag} ${it.value.clivalue.toString().replaceAll(/(?:^\s+|\s+$)/, '')}" + }.join(' ').trim() + } + return 1 +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/workflows/conf/spades_only.config Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,24 @@ +params { + workflow_built_by = 'Kranti.Konganti@fda.hhs.gov' + workflow_version = '0.1.0' + spades_run = true + spades_isolate = false + spades_sc = false + spades_meta = false + spades_bio = false + spades_corona = false + spades_rna = false + spades_plasmid = false + spades_metaviral = false + spades_metaplasmid = false + spades_rnaviral = false + spades_iontorrent = false + spades_only_assembler = false + spades_careful = false + spades_cov_cutoff = false + spades_k = false + spades_hmm = false + fq_filter_by_len = 75 + fq_suffix = '_R1_001.fastq.gz' + fq2_suffix = '_R2_001.fastq.gz' +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/workflows/nanofactory.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,185 @@ +// +// Start nanofactory workflow. Since this is a special +// case workflow wherein most of the bioinformatics +// tools are not used, there won't be any modules or +// subworkflows and therefore all the processes +// reside here. +// + +// Include any necessary methods. +include { addPadding; summaryOfParams; stopNow} \ + from "${params.routines}" + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + PROCESS DEFINITIONS FOR NANOFACTORY +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +process SETPUBLISHDIR { + label 'process_femto' + module (params.enable_module ? params.enable_module : null) + conda (params.enable_conda ? params.enable_conda : null) + + input: + val options + + output: + stdout + + shell: + ''' + project_setup.py -s !{options.sample_sheet} \ + !{options.alt_settings} !{options.verbose} -b + ''' +} + +process PROJECTSETUP { + label 'process_femto' + publishDir "${publish_dir.trim()}", mode: 'copy', overwrite: false + module (params.enable_module ? params.enable_module : null) + conda (params.enable_conda ? params.enable_conda : null) + + input: + val options + val publish_dir + + output: + stdout + + script: + params.publish_dir = "${publish_dir.trim()}" + + shell: + ''' + project_setup.py -y -s !{options.sample_sheet} !{options.alt_settings} \ + !{options.purge} !{options.runtype} !{options.logfile} \ + !{options.loglevel} !{options.verbose} !{options.nocopy} \ + !{options.fix_existing} + + cat < original_source.txt + ''' +} + +process TRIMDEMUX { + label 'process_pico' + module (params.enable_module ? params.enable_module : null) + conda (params.enable_conda ? params.enable_conda : null) + cpus "${params.guppy_threads}" + + input: + val options + val original_source + + output: + path 'source.txt' + + shell: + ''' + trim_demux.py -s !{options.sample_sheet} !{options.verbose} \ + !{options.alt_settings} !{options.guppy_config} -t !{options.guppy_threads} + ''' +} + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + WORKFLOW ENTRY POINT +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +workflow NANOFACTORY { + + if ( params.help ) { + log.info help() + } else if ( params.sample_sheet == null || + params.sample_sheet.length() == 0 ) { + + log.info help() + stopNow("Please provide absolute path to a JSON formatted sample sheet using the\n" + + "--sample_sheet option.") + } else { + log.info summaryOfParams() + + options = Channel.empty() + Channel + .from(setOptions()) + .set { options } + + take: + options + + main: + SETPUBLISHDIR(options) + PROJECTSETUP(options, SETPUBLISHDIR.out) + TRIMDEMUX(options, PROJECTSETUP.out) + } +} + + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + THE END +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + HELPER METHODS FOR NANOFACTORY WORKFLOW +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +def setOptions() { + + Map options = [:] + + options['sample_sheet'] ?= "${params.sample_sheet}" + options['verbose'] = params.verbose ? "-v" : "" + options['alt_settings'] = params.global_settings ? "-c ${params.global_settings}" : "" + options['purge'] = params.setup_purge_existing ? "-p" : "" + options['logfile'] = params.log_file ? "-l ${params.log_file}" : "" + options['loglevel'] = params.log_level ? "--loglevel ${params.log_level}" : "" + options['nocopy'] = params.setup_nocopy ? "--nocopy" : "" + options['runtype'] = params.setup_runtype ? "-r ${params.setup_runtype}" : "" + options['fix_existing'] = params.setup_fix_existing ? "-f" : "" + options['guppy_config'] = params.guppy_config ? " -g ${params.guppy_config}" : "" + options['mode'] = params.mode ? "-m ${params.mode}" : "-m prod" + options['mail_group'] = params.mail_group ? "-g ${params.mail_group}" : "-g stakeholders" + options['guppy_threads'] = params.guppy_threads ? "${params.guppy_threads}" : 1 + options['pad'] = pad.toInteger() + options['nocapitalize'] = true + + return options +} + +def help() { + + Map helptext = [:] + + helptext['help'] = true + helptext['nocapitalize'] = true + helptext['Workflow'] = "${params.pipeline}" + helptext['Author'] = "${params.workflow_author}" + helptext['Version'] = "${params.workflow_version}\n" + helptext['Usage'] = "cpipes --pipeline nanofactory [options]\n" + helptext['Required'] = "" + helptext['--sample_sheet'] = "The JSON-formatted sample sheet for this run. Normally provided by Pore Refiner.\n" + helptext['Other options'] = "" + helptext['--global_settings'] = "An alternate global settings file. If not present the installed default will be used." + helptext['--log_file'] = "Path and file name to a log file relative to the project directory (Default: 'logs/workflow.log')" + helptext['--log_level'] = "One of 'debug', 'info', 'warning', 'error', 'fatal' (Default: 'info')" + helptext['--mode'] = "Set the run mode. One of 'dev', 'test', 'stage', or 'prod' (Default: 'prod')" + helptext['--verbose'] = "Use to enable more verbose console output from each tool\n" + helptext['Project setup options'] = "" + helptext['--disable_project_setup'] = "Do not do project setup (Default: setup is enabled)" + helptext['--setup_purge_existing'] = "Before setting up the project area delete any existing files (Default: don't purge)" + helptext['--setup_nocopy'] = "During setup, do NOT copy the original data files to the scrach location (Default: copy)" + helptext['--setup_runtype'] = "Set things up for the indicated run type (Currently not used)" + helptext['--setup_runtype'] = "Set things up for the indicated run type (Currently not used)" + helptext['--enable_module'] = "Software environment module. Ex: --enable_module 'nanofactory/current'" + helptext['--enable_conda'] = "CONDA environment module. Ex: --enable_conda nanofactory\n" + helptext['Help options'] = "" + helptext['--help'] = "Display this message.\n" + + return addPadding(helptext) +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.4.2/workflows/spades_only.nf Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,130 @@ +// Define any required imports for this specific workflow +import java.nio.file.Paths +import nextflow.file.FileHelper + +// Include any necessary methods +include { \ + summaryOfParams; stopNow; fastqEntryPointHelp; sendMail; \ + addPadding; wrapUpHelp } from "${params.routines}" +include { spadesHelp } from "${params.toolshelp}${params.fs}spades" + + +// Exit if help requested before any subworkflows +if (params.help) { + log.info help() + exit 0 +} + +// Include any necessary modules and subworkflows +include { PROCESS_FASTQ } from "${params.subworkflows}${params.fs}process_fastq" +include { SPADES_ASSEMBLE } from "${params.modules}${params.fs}spades${params.fs}assemble${params.fs}main" +include { DUMP_SOFTWARE_VERSIONS } from "${params.modules}${params.fs}custom${params.fs}dump_software_versions${params.fs}main" + + + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + INPUTS AND ANY CHECKS FOR THE CENTRIFLAKEN-HY WORKFLOW +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +def spades_custom_hmm = (params.spades_hmm ? file ( "${params.spades_hmm}" ) : false) +def reads_platform = 0 + +reads_platform += (params.input ? 1 : 0) + +if (spades_custom_hmm && !spades_custom_hmm.exists()) { + stopNow("Please check if the following SPAdes' custom HMM directory\n" + + "path is valid:\n${params.spades_hmm}\nCannot proceed further!") +} + +if (reads_platform < 1 || reads_platform == 0) { + stopNow("Please mention at least one absolute path to input folder which contains\n" + + "FASTQ files sequenced using the --input option.\n" + + "Ex: --input (Illumina or Generic short reads in FASTQ format)") +} + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + RUN THE CENTRIFLAKEN-HY WORKFLOW +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +workflow SPADES_ONLY { + main: + ch_dummy = Channel.fromPath("${params.dummyfile}") + ch_dummy2 = Channel.fromPath("${params.dummyfile2}") + + log.info summaryOfParams() + + PROCESS_FASTQ() + .processed_reads + .set { ch_processed_reads } + + PROCESS_FASTQ + .out + .versions + .set { software_versions } + + // As of 06/02/2022, with the upcoming newer versions of NextFlow, we will be able to do + // allowNull: true for both input and output, but until then, we have to use dummy files. + // and work arounds. + // https://github.com/nextflow-io/nextflow/pull/2893 + + SPADES_ASSEMBLE ( + ch_processed_reads + .combine(ch_dummy) + .combine(ch_dummy2) + ) + + SPADES_ASSEMBLE + .out + .assembly + .set { ch_assembly } + + software_versions + .mix ( SPADES_ASSEMBLE.out.versions.ifEmpty(null) ) + .set { software_versions } + + + DUMP_SOFTWARE_VERSIONS ( + software_versions + .unique() + .collectFile(name: 'collected_versions.yml') + ) +} + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + ON COMPLETE, SHOW GORY DETAILS OF ALL PARAMS WHICH WILL BE HELPFUL TO DEBUG +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +workflow.onComplete { + if (workflow.success) { + sendMail() + } +} + +workflow.onError { + sendMail() +} + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + HELPER METHODS FOR CENTRIFLAKEN-HY WORKFLOW +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +def help() { + + Map helptext = [:] + + helptext.putAll ( + fastqEntryPointHelp() + + spadesHelp(params).text + + wrapUpHelp() + ) + + return addPadding(helptext) +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hfp_centriflaken.xml Fri May 29 13:27:47 2026 +0000 @@ -0,0 +1,231 @@ +<tool id="hfp_centriflaken_awsbatch" name="centriflaken" version="0.4.2+awsbatch"> + <description>An automated pipeline to generate a MAG of interest (E.coli or Salmonella) and perform serotyping.</description> + <requirements> + <container type="docker">quay.io/galaxytrakr/mulled-v2-ebd88135862aa647eeae73d4d8e6ea8ec81245cd:v5.0</container> + </requirements> + <version_command>nextflow -version</version_command> + <command detect_errors="exit_code"><![CDATA[ + export MAMBA_ROOT_PREFIX="/server/galaxy/data/nextflow-micromamba-cache"; + export NXF_HOME=\$(pwd)"/.nextflow-home"; + input_path=\$(pwd)"/cpipes-input"; + mkdir -p "\${input_path}" || exit 1; + #import re + #if (str($input_read_type_cond.input_read_type) == "single_long"): + #for _, $unpaired in enumerate($input_read_type_cond.input): + #set read1 = str($unpaired.name) + #if not str($unpaired.name).endswith(('.fastq', '.fastq.gz')): + #set read1_ext = re.sub('fastqsanger', 'fastq', str($unpaired.ext)) + #set read1 = str($unpaired.name) + str('.') + $read1_ext + #end if + ln -sf '$unpaired' "\${input_path}/$read1"; + #end for + #elif (str($input_read_type_cond.input_read_type) == "paired"): + #for _, $pair in enumerate($input_read_type_cond.input_pair) + #set read_R1 = re.sub('\:forward', '_forward', str($pair.forward.name)) + #set read_R2 = re.sub('\:reverse', '_reverse', str($pair.reverse.name)) + #set read_R1_ext = re.sub('fastqsanger', 'fastq', str($pair.forward.ext)) + #set read_R2_ext = re.sub('fastqsanger', 'fastq', str($pair.reverse.ext)) + #if not str($pair.forward.name).endswith(('.fastq', '.fastq.gz')): + #set read_R1 = $read_R1 + str('.') + $read_R1_ext + #end if + #if not str($pair.reverse.name).endswith(('.fastq', '.fastq.gz')): + #set read_R2 = $read_R2 + str('.') + $read_R2_ext + #end if + ln -sf '$pair.forward' "\${input_path}/$read_R1"; + ln -sf '$pair.reverse' "\${input_path}/$read_R2"; + #end for + #end if + $__tool_directory__/0.4.2/cpipes + --pipeline $input_read_type_cond.pipeline_cond.pipeline + #if ($input_read_type_cond.pipeline_cond.pipeline == "centriflaken"): + --fq_single_end true + --flye_genome_size '${genome_size}' + #if ($input_read_type_cond.pipeline_cond.long_read_platform == "nanopore_corr"): + --flye_nano_corr true --flye_nano_raw false + #elif ($input_read_type_cond.pipeline_cond.long_read_platform == "nanopore_hq"): + --flye_nano_hq true --flye_nano_raw false + #elif ($input_read_type_cond.pipeline_cond.long_read_platform == "pacbio_raw"): + --flye_pacbio_raw true --flye_nano_raw false + #elif ($input_read_type_cond.pipeline_cond.long_read_platform == "pacbio_corr"): + --flye_pacbio_corr true --flye_nano_raw false + #elif ($input_read_type_cond.pipeline_cond.long_read_platform == "pacbio_hifi"): + --flye_pacbio_hifi true --flye_nano_raw false + #end if + #elif ($input_read_type_cond.pipeline_cond.pipeline == "centriflaken_hy"): + #if (str($input_read_type_cond.input_read_type) == "single_long"): + --fq_single_end true + #elif (str($input_read_type_cond.input_read_type) == "paired"): + --fq_single_end false --fq2_suffix '${input_read_type_cond.fq2_suffix}' + #end if + #end if + --input \${input_path} + --output cpipes-output + --fq_suffix '${input_read_type_cond.fq_suffix}' + #if ($fq_filter_by_len != ""): + --fq_filter_by_len $fq_filter_by_len + #end if + --fq_filename_delim '${fq_filename_delim}' + --fq_filename_delim_idx $fq_filename_delim_idx + --centrifuge_extract_bug '${centrifuge_extract_bug}' + #if (str($input_read_type_cond.pipeline_cond.rm_dup_seqs) == "true"): + --seqkit_rmdup_run true + #end if + -profile stdkondagac; + mv "./cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-multiqc/CPIPES-Report_multiqc_report.html" "./multiqc_report.html" || exit 1; + mv "./cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-results/kraken2_extract_contigs" "kraken2_extract_contigs" || exit 1; + ]]></command> + <inputs> + <conditional name="input_read_type_cond"> + <param name="input_read_type" type="select" label="Select the read collection type"> + <option value="single_long" selected="true">Unpaired reads (i.e. Single-End short reads or Long reads)</option> + <option value="paired">Paired-End reads</option> + </param> + <when value="single_long"> + <param name="input" type="data_collection" collection_type="list" format="fastq,fastq.gz" + label="Dataset list of unpaired short reads or long reads" /> + <conditional name="pipeline_cond"> + <param name="pipeline" type="select" label="CPIPES Workflow name" + help="centriflaken: for long reads (Nanopore or PacBio). centriflaken_hy: for unpaired short reads. Default: centriflaken"> + <option value="centriflaken" selected="true">centriflaken</option> + <option value="centriflaken_hy">centriflaken_hy</option> + </param> + <when value="centriflaken"> + <param name="long_read_platform" type="select" label="Mention long read sequencing platform and type"> + <option value="nanopore_raw" selected="true">Nanopore raw reads, pre-Guppy5 (<20% error)</option> + <option value="nanopore_corr">Nanopore reads that were corrected with other methods (<3% error)</option> + <option value="nanopore_hq">Nanopore high-quality reads, Guppy5+ SUP or Q20 (5% error)</option> + <option value="pacbio_raw">PacBio regular CLR reads (<20% error)</option> + <option value="pacbio_corr">PacBio reads that were corrected with other methods (<3% error)</option> + <option value="pacbio_hifi">PacBio HiFi reads (<1% error)</option> + </param> + <param name="rm_dup_seqs" type="select" label="Remove duplicate sequences" + help="THIS OPTION IS IGNORED IF THE INPUT READS ARE LONG READS."> + <option value="NA" selected="true">N/A</option> + </param> + </when> + <when value="centriflaken_hy"> + <param name="long_read_platform" type="select" label="Mention long read sequencing platform and type" + help="THIS OPTION IS IGNORED IF THE INPUT READS ARE SHORT READS."> + <option value="NA" selected="true">N/A</option> + </param> + <param name="rm_dup_seqs" type="select" label="Remove duplicate sequences" + help="Selecting yes will compare sequence content and remove identical sequences i.e. only the first occured sequence record will be saved."> + <option value="true">yes</option> + <option value="false" selected="true">no</option> + </param> + </when> + </conditional> + <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the Unpaired FASTQ"/> + </when> + <when value="paired"> + <param name="input_pair" type="data_collection" collection_type="list:paired" format="fastq,fastq.gz" label="List of Dataset pairs" /> + <conditional name="pipeline_cond"> + <param name="pipeline" type="select" label="CPIPES Workflow name" + help="Auto selected centriflaken_hy workflow for paired-end short reads."> + <option value="centriflaken_hy" selected="true">centriflaken_hy</option> + </param> + <when value="centriflaken_hy"> + <param name="long_read_platform" type="select" label="Mention long read sequencing platform and type" + help="THIS OPTION IS IGNORED IF THE INPUT READS ARE SHORT READS."> + <option value="NA" selected="true">N/A</option> + </param> + <param name="rm_dup_seqs" type="select" label="Remove duplicate sequences" + help="Selecting yes will compare sequence content and remove identical sequences i.e. only the first occured sequence record will be saved."> + <option value="true">yes</option> + <option value="false" selected="true">no</option> + </param> + </when> + </conditional> + <param name="fq_suffix" value="_R1_001.fastq.gz" type="text" label="Suffix of the R1 FASTQ"/> + <param name="fq2_suffix" value="_R2_001.fastq.gz" type="text" label="Suffix of the R2 FASTQ"/> + </when> + </conditional> + <param name="fq_filter_by_len" optional="true" value="" type="integer" label="Enter minimum read length to retain before starting the analysis" + help="Keep this option empty to use default values. Default for centriflaken (long reads) is 4000 bp and for centriflaken_hy (short reads) is 75 bp."/> + <param name="fq_filename_delim" type="text" value="_" label="File name delimitor by which samples are grouped together (--fq_filename_delim)" + help="This is the delimitor by which samples are grouped together to display in the final MultiQC report. For example, if your input data sets are mango_replicate1.fastq.gz, mango_replicate2.fastq.gz, orange_replicate1_maryland.fastq.gz, orange_replicate2_maryland.fastq.gz, then to create 2 samples mango and orange, the value for --fq_filename_delim would be _ (underscore) and the value for --fq_filename_delim_idx would be 1, since you want to group by the first word (i.e. mango or orange) after splitting the filename based on _ (underscore)."/> + <param name="fq_filename_delim_idx" type="integer" value="1" label="File name delimitor index (--fq_filename_delim_idx)" /> + <param name="centrifuge_extract_bug" type="text" value="Escherichia coli" label="Reads belonging to this taxa are extracted and a MAG is generated to allow for serotyping"/> + <param name="genome_size" type="text" optional="true" value="5.5m" label="Estimated genome size" help="For example, 5m or 2.6g."> + <validator type="regex" message="Genome size must be a float or integer, optionally followed by the a unit prefix (kmg)">^([0-9]*[.])?[0-9]+[kmg]?$</validator> + </param> + <!-- <param name="runtime_profile" type="select" label="Run time profile"> + <option value="kondagac" selected="true">conda</option> + <option value="cingularitygac">singularity</option> + </param> --> + </inputs> + <outputs> + <data name="multiqc_report" format="html" label="${input_read_type_cond.pipeline_cond.pipeline}: MultiQC Report on ${on_string}" from_work_dir="multiqc_report.html"/> + <collection name="assembled_mags" type="list" label="${input_read_type_cond.pipeline_cond.pipeline}: Assembled MAGs on ${on_string}"> + <discover_datasets pattern="(?P<name>.*)\.assembly_filtered_contigs\.fasta" ext="fasta" directory="kraken2_extract_contigs"/> + </collection> + </outputs> + <tests> + <!--Test 01: long reads--> + <test expect_num_outputs="2"> + <param name="input"> + <collection type="list"> + <element name="FAL11127.fastq.gz" value="FAL11127.fastq.gz" /> + <element name="FAL11341.fastq.gz" value="FAL11341.fastq.gz" /> + <element name="FAL11342.fastq.gz" value="FAL11342.fastq.gz" /> + </collection> + </param> + <param name="fq_suffix" value=".fastq.gz"/> + <output name="multiqc_report" file="multiqc_report.html" ftype="html" compare="sim_size"/> + <!-- <output name="assembled_mags" file="FAL11127.assembly_filtered.contigs.fasta" ftype="fasta" compare="sim_size"/> --> + </test> + </tests> + <help><![CDATA[ + +.. class:: infomark + +**Purpose** + +Centriflaken suite of automated data analysis pipelines are based on Nextflow DSL2 developed at CFSAN, FDA. These pipelines allow rapid +and effective construction of metagenomic assembled genomes (MAGs) to enable bacterial source-tracking. It is based on methods described in our +previous publication (Maguire *et al*, 2021. doi: https://doi.org/10.1371/journal.pone.0245172). + +---- + +.. class:: infomark + +**Testing and Validation** + +The CPIPES - Centriflaken Nextflow pipeline has been wrapped to make it work in Galaxy. It takes in either paired or unpaired short reads or long reads, generates MAGs and performs +in silico-based analysis (i.e., virulence gene finding). Additionally, AMR gene finding analysis is also included in Centriflaken and performed on MAGs +of interest. The final summary plots and tables can be downloaded from the provided MultiQC HTML report generated as part of the pipeline. +The Centriflaken pipeline was validated with data from our previously published method (Maguire *et al*, 2021. doi: https://doi.org/10.1371/journal.pone.0245172) and was able to replicate the detection +and classification of STECs for each sample. We tested the pipeline with Nanopore data obtained from 21 additional enriched samples from +irrigation water and was able to perform the entire precision metagenomics analysis in less than 5 hours for all of them. All the original testing and validation was +done on the command line on the CFSAN Raven2 HPC Cluster. + + +---- + +.. class:: infomark + +**Outputs** + +The main output files are: + + :: + + - MultiQC Report: Contains a brief summary report including any serotyping and AMR result tables. + Please note that due to MultiQC customizations, the preview (eye icon) will not + work within Galaxy for the MultiQC report. Please download the file by clicking + on the floppy icon and view it in your browser on your local desktop/workstation. + - Final assembly: contains contigs and possibly scaffolds. + + ]]></help> + <citations> + <citation type="bibtex"> + @misc{gitlabCPIPES, + author = {Konganti, Kranti}, + year = {2022}, + title = {CPIPES - Centriflaken}, + publisher = {GitLab}, + journal = {GitLab repository}, + url = {https://cfsan-git.fda.gov/Kranti.Konganti/cpipes}} + </citation> + </citations> +</tool>