kkonganti@3: <tool id="cfsan_cronology" name="cronology" version="0.1.0">
kkonganti@0:     <description>An automated workflow for Cronobacter isolate assembly, sequence typing and traceback.</description>
kkonganti@0:     <requirements>
kkonganti@1:         <requirement type="package" version="23.04">nextflow</requirement>
kkonganti@1:         <requirement type="package" version="1.0.0">micromamba</requirement>
kkonganti@1:         <requirement type="package">graphviz</requirement>
kkonganti@0:     </requirements>    
kkonganti@0:     <version_command>nextflow -version</version_command>
kkonganti@0:     <command detect_errors="exit_code"><![CDATA[
kkonganti@0: 	mkdir -p cpipes-input || exit 1;
kkonganti@0:     pwd_path=\$(pwd);
kkonganti@0:     #import re
kkonganti@0:     #if (str($input_read_type_cond.input_read_type) == "single_long"):
kkonganti@0: 	    #for _, $unpaired in enumerate($input_read_type_cond.input):
kkonganti@0:             #set read1 = str($unpaired.name)
kkonganti@0:             #if not str($unpaired.name).endswith(('.fastq', '.fastq.gz')):
kkonganti@0:                 #set read1_ext = re.sub('fastqsanger', 'fastq', str($unpaired.ext))
kkonganti@0:                 #set read1 = str($unpaired.name) + str('.') + $read1_ext
kkonganti@0:             #end if
kkonganti@0:             ln -sf '$unpaired' './cpipes-input/$read1';
kkonganti@0: 	    #end for
kkonganti@0:     #elif (str($input_read_type_cond.input_read_type) == "paired"):
kkonganti@0: 	    #for _, $pair in enumerate($input_read_type_cond.input_pair)
kkonganti@0:             #set read_R1 = re.sub('\:forward', '_forward', str($pair.forward.name))
kkonganti@0:             #set read_R2 = re.sub('\:reverse', '_reverse', str($pair.reverse.name))
kkonganti@0:             #set read_R1_ext = re.sub('fastqsanger', 'fastq', str($pair.forward.ext))
kkonganti@0:             #set read_R2_ext = re.sub('fastqsanger', 'fastq', str($pair.reverse.ext))
kkonganti@0:             #if not str($pair.forward.name).endswith(('.fastq', '.fastq.gz')):
kkonganti@0: 	            #set read_R1 = $read_R1 + str('.') + $read_R1_ext
kkonganti@0:             #end if
kkonganti@0:             #if not str($pair.reverse.name).endswith(('.fastq', '.fastq.gz')):
kkonganti@0:                 #set read_R2 = $read_R2 + str('.') + $read_R2_ext
kkonganti@0:             #end if
kkonganti@0: 	        ln -sf '$pair.forward' './cpipes-input/$read_R1';
kkonganti@0: 	        ln -sf '$pair.reverse' './cpipes-input/$read_R2';
kkonganti@0: 	    #end for
kkonganti@0:     #end if
kkonganti@0: 	$__tool_directory__/0.1.0/cpipes
kkonganti@0:     --pipeline cronology
kkonganti@0:     --input \${pwd_path}/cpipes-input
kkonganti@0: 	--output \${pwd_path}/cpipes-output
kkonganti@0:     --fq_suffix '${input_read_type_cond.fq_suffix}'
kkonganti@0:     #if (str($input_read_type_cond.input_read_type) == "single_long"):
kkonganti@0:         --fq_single_end true
kkonganti@0:     #elif (str($input_read_type_cond.input_read_type) == "paired"):
kkonganti@0:         --fq_single_end false --fq2_suffix '${input_read_type_cond.fq2_suffix}'
kkonganti@0:     #end if
kkonganti@0:     --ref_acc $refgenome
kkonganti@0:     --tuspy_n $tuspy_n
kkonganti@0: 	--fq_filename_delim '${fq_filename_delim}'
kkonganti@0: 	--fq_filename_delim_idx $fq_filename_delim_idx
kkonganti@0: 	-profile kondagac;
kkonganti@0:     mv './cpipes-output/cronology-multiqc/multiqc_report.html' './multiqc_report.html' > /dev/null 2>&1 || exit 1;
kkonganti@0:     mv './cpipes-output/mashtree/hitsTree.dnd' './hitsTree.dnd' > /dev/null 2>&1 || exit 1;
kkonganti@0:     ]]></command>
kkonganti@0:     <inputs>
kkonganti@0:         <conditional name="input_read_type_cond">
kkonganti@0:             <param name="input_read_type" type="select" label="Select the read collection type">
kkonganti@0:                 <option value="single_long" selected="true">Single-End short reads</option>
kkonganti@0:                 <option value="paired">Paired-End short reads</option>
kkonganti@0:             </param>
kkonganti@0:             <when value="single_long">
kkonganti@0:                 <param name="input" type="data_collection" collection_type="list" format="fastq,fastq.gz"
kkonganti@0:                     label="Dataset list of unpaired short reads or long reads" />
kkonganti@0:                 <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the Single-End FASTQ"/>
kkonganti@0:             </when>
kkonganti@0:             <when value="paired">
kkonganti@0:                 <param name="input_pair" type="data_collection" collection_type="list:paired" format="fastq,fastq.gz" label="List of Dataset pairs" />
kkonganti@0:                 <param name="fq_suffix" value="_R1_001.fastq.gz" type="text" label="Suffix of the R1 FASTQ"
kkonganti@0:                     help="For any data sets downloaded from NCBI into Galaxy, change this to _forward.fastq.gz suffix."/>
kkonganti@0:                 <param name="fq2_suffix" value="_R2_001.fastq.gz" type="text" label="Suffix of the R2 FASTQ"
kkonganti@0:                     help="For any data sets downloaded from NCBI into Galaxy, change this to _reverse.fastq.gz suffix."/>
kkonganti@0:             </when>
kkonganti@0:         </conditional>
kkonganti@0:         <param name="refgenome" optional="true" value="GCF_003516125" type="text"
kkonganti@0:                 label="NCBI reference genome accession"
kkonganti@3:                 help="Is the reference genome other than Cronobacter sakazakii? Reference genome FASTA is used as a model for gene prediction. DO NOT ENTER THE DECIMAL PART (Ex: GCF_003516125.1)." />
kkonganti@0:         <param name="tuspy_n" optional="true" value="10" type="integer" label="Enter the number of top unique hits to retain after initial MASH screen step"
kkonganti@0:             help="These hits will be used to build a genome distance based tree for your experiment run. Default value of 2 is suitable for almost all scenarios."/>
kkonganti@0:         <param name="fq_filename_delim" type="text" value="_" label="File name delimitor by which samples are grouped together (--fq_filename_delim)" 
kkonganti@0:             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)."/>
kkonganti@0:         <param name="fq_filename_delim_idx" type="integer" value="1" label="File name delimitor index (--fq_filename_delim_idx)" />
kkonganti@0:     </inputs>
kkonganti@0:     <outputs>
kkonganti@0:         <data name="multiqc_report" format="html" label="cronology: MultiQC Report on ${on_string}" from_work_dir="multiqc_report.html"/>
kkonganti@0:         <data name="mashtree" format="nwk" label="cronology: Genome distance based tree on ${on_string}" from_work_dir="hitsTree.dnd"/>
kkonganti@0:         <collection name="itol_metadata" type="list" label="cronology: iTOL Metadata: ${on_string}">
kkonganti@3:             <discover_datasets pattern="(?P&lt;name&gt;.*)\.txt" ext="txt" directory="./cpipes-output/cat_unique" match_relative_path="true" />
kkonganti@0:         </collection>
kkonganti@0:         <collection name="gene_models" type="list" label="cronology: Predicted gene models: ${on_string}">
kkonganti@3:             <discover_datasets pattern="(?P&lt;name&gt;.*)\.gff" ext="gff" directory="./cpipes-output/prokka" recurse="true" match_relative_path="true" />
kkonganti@0:         </collection>
kkonganti@0:         <collection name="assemblies" type="list" label="cronology: Polished genome assemblies: ${on_string}">
kkonganti@3:             <discover_datasets pattern="(?P&lt;name&gt;.*)\.fa" ext="fa" directory="./cpipes-output/polypolish" match_relative_path="true" />
kkonganti@0:         </collection>
kkonganti@0:     </outputs>
kkonganti@0:     <tests>
kkonganti@0:         <!--Test 01: long reads-->
kkonganti@0:         <test expect_num_outputs="2">
kkonganti@0:             <param name="input">
kkonganti@0:                 <collection type="list">
kkonganti@0:                     <element name="FAL11127.fastq.gz" value="FAL11127.fastq.gz" />
kkonganti@0:                     <element name="FAL11341.fastq.gz" value="FAL11341.fastq.gz" />
kkonganti@0:                     <element name="FAL11342.fastq.gz" value="FAL11342.fastq.gz" />
kkonganti@0:                 </collection>
kkonganti@0:             </param>
kkonganti@0:             <param name="fq_suffix" value=".fastq.gz"/>
kkonganti@0:             <output name="multiqc_report" file="multiqc_report.html" ftype="html" compare="sim_size"/>
kkonganti@0:             <!-- <output name="assembled_mags" file="FAL11127.assembly_filtered.contigs.fasta" ftype="fasta" compare="sim_size"/> -->
kkonganti@0:         </test>
kkonganti@0:     </tests>
kkonganti@0:     <help><![CDATA[
kkonganti@0: 
kkonganti@0: .. class:: infomark
kkonganti@0: 
kkonganti@0: **Purpose**
kkonganti@0: 
kkonganti@0: cronology is an automated workflow to assign Salmonella serotype based on NCBI Pathogen Detection Project for Salmonella. 
kkonganti@0: It uses MASH to reduce the search space followed by additional genome filtering with sourmash. It then performs genome based 
kkonganti@0: alignment with kma followed by count generation using salmon. This workflow can be used to analyze shotgun metagenomics 
kkonganti@0: datasets, quasi-metagenomic datasets (enriched for Salmonella) and target enriched datasets (enriched with molecular baits specific for Salmonella) 
kkonganti@0: and is especially useful in a case where a sample is of multi-serovar mixture.
kkonganti@0: 
kkonganti@0: It is written in Nextflow and is part of the modular data analysis pipelines (CFSAN PIPELINES or CPIPES for short) at CFSAN.
kkonganti@0: 
kkonganti@0: 
kkonganti@0: ----
kkonganti@0: 
kkonganti@0: .. class:: infomark
kkonganti@0: 
kkonganti@0: **Testing and Validation**
kkonganti@0: 
kkonganti@0: The CPIPES - cronology Nextflow pipeline has been wrapped to make it work in Galaxy. It takes in either paired or unpaired short reads list as an input 
kkonganti@1: and performs read quality control followed by de novo assembly, gene prediction and annotation, sequence typing and whole genome distance based clustering.
kkonganti@1: All the testing has been done on the command line on the CFSAN Raven2 HPC Cluster.
kkonganti@0: 
kkonganti@0: 
kkonganti@0: ----
kkonganti@0: 
kkonganti@0: .. class:: infomark
kkonganti@0: 
kkonganti@0: **Outputs**
kkonganti@0: 
kkonganti@1: The main output files are:
kkonganti@0: 
kkonganti@0:     ::
kkonganti@0: 
kkonganti@0:         - MultiQC Report: Contains a brief summary report including any serotyping and AMR result tables.
kkonganti@0:                           Please note that due to MultiQC customizations, the preview (eye icon) will not
kkonganti@0:                           work within Galaxy for the MultiQC report. Please download the file by clicking
kkonganti@0:                           on the floppy icon and view it in your browser on your local desktop/workstation.
kkonganti@0:                           You can export the tables and plots from the downloaded MultiQC report.
kkonganti@1:         - Polished de novo assemblies (FASTA) for each sample.
kkonganti@1:         - Genome annotations (GFF) for each sample.
kkonganti@1:         - Whole genome distance based clustering tree (Newick).
kkonganti@1:         - Additional metadata useful for uploading the Newick tree into iTOL. 
kkonganti@0: 
kkonganti@0:   ]]></help>
kkonganti@0:     <citations>
kkonganti@0:         <citation type="bibtex">
kkonganti@0:             @article{cronology,
kkonganti@0:             author = {Konganti, Kranti},
kkonganti@4:             year = {2024},
kkonganti@4:             month = {May},
kkonganti@1:             title = {cronology: An automated workflow for Cronobacter isolate assembly, sequence typing and traceback},
kkonganti@1:             journal = {Unpublished},
kkonganti@4:             doi = {xx.xxxx/xxxxx.2024.xxxxxxxxxx},
kkonganti@1:             url = {https://github.com/CFSAN-Biostatistics/cronology}}
kkonganti@0:         </citation>
kkonganti@0:     </citations>
kkonganti@0: </tool>