Mercurial > repos > kkonganti > hfp_nowayout
diff 0.5.0/readme/centriflaken_hy.md @ 0:97cd2f532efe
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| author | kkonganti |
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| date | Mon, 31 Mar 2025 14:50:40 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.5.0/readme/centriflaken_hy.md Mon Mar 31 14:50:40 2025 -0400 @@ -0,0 +1,367 @@ +# 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.** + +--- + +### **centriflaken_hy** + +--- +`centriflaken_hy` is a variant of the original `centriflaken` pipeline but for Illumina short reads either single-end or paired-end. + +#### Workflow Usage + +```bash +module load cpipes/0.4.0 + +cpipes --pipeline centriflaken_hy [options] +``` + +Example: Run the default `centriflaken_hy` pipeline with taxa of interest as *E. coli*. + +```bash +cd /hpc/scratch/$USER +mkdir nf-cpipes +cd nf-cpipes +cpipes --pipeline centriflaken_hy --input /path/to/illumina/fastq/dir --output /path/to/output --user_email 'Kranti.Konganti@fda.hhs.gov' +``` + +Example: Run the `centriflaken_hy` pipeline with taxa of interest as *Salmonella*. In this mode, `SerotypeFinder` tool will be replaced with `SeqSero2` tool. + +```bash +cd /hpc/scratch/$USER +mkdir nf-cpipes +cd nf-cpipes +cpipes --pipeline centriflaken_hy --centrifuge_extract_bug 'Salmonella' --input /path/to/illumina/fastq/dir --output /path/to/output --user_email 'Kranti.Konganti@fda.hhs.gov' +``` + +#### `centriflaken_hy` Help + +```text +[Kranti.Konganti@login2-slurm ]$ cpipes --pipeline centriflaken_hy --help +N E X T F L O W ~ version 21.12.1-edge +Launching `/home/Kranti.Konganti/apps/cpipes/cpipes` [soggy_curie] - revision: 72db279311 +================================================================================ + (o) + ___ _ __ _ _ __ ___ ___ + / __|| '_ \ | || '_ \ / _ \/ __| +| (__ | |_) || || |_) || __/\__ \ + \___|| .__/ |_|| .__/ \___||___/ + | | | | + |_| |_| +-------------------------------------------------------------------------------- +A collection of modular pipelines at CFSAN, FDA. +-------------------------------------------------------------------------------- +Name : CPIPES +Author : Kranti.Konganti@fda.hhs.gov +Version : 0.4.0 +Center : CFSAN, FDA. +================================================================================ + +Workflow : centriflaken_hy + +Author : Kranti.Konganti@fda.hhs.gov + +Version : 0.4.0 + + +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. +``` + +### **BETA** + +--- +The development of the modular structure and flow is an ongoing effort and may change depending on assessment of various computational topics and other considerations.