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Merge pull request #30 from FelixKrueger/bowtie2
Added Bowtie2 module and test workflow
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4 changed files with 122 additions and 0 deletions
52
tools/bowtie2/main.nf
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52
tools/bowtie2/main.nf
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nextflow.preview.dsl=2
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params.genome = ''
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process BOWTIE2 {
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// depending on the genome used one might want/need to adjust the memory settings.
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// For the E. coli test data this is probably not required
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// label 'bigMem'
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// label 'multiCore'
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input:
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tuple val(name), path(reads)
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val (outdir)
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val (bowtie2_args)
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val (verbose)
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output:
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path "*bam", emit: bam
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path "*stats.txt", emit: stats
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publishDir "$outdir/bowtie2",
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mode: "copy", overwrite: true
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script:
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if (verbose){
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println ("[MODULE] BOWTIE2 ARGS: " + bowtie2_args)
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}
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cores = 4
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readString = ""
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// Options we add are
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bowtie2_options = bowtie2_args
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bowtie2_options += " --no-unal " // We don't need unaligned reads in the BAM file
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// single-end / paired-end distinction. Might also be handled via params.single_end
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if (reads instanceof List) {
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readString = "-1 " + reads[0] + " -2 " + reads[1]
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}
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else {
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readString = "-U " + reads
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}
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index = params.genome["bowtie2"]
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bowtie2_name = name + "_" + params.genome["name"]
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"""
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bowtie2 -x ${index} -p ${cores} ${bowtie2_options} ${readString} 2>${bowtie2_name}_bowtie2_stats.txt | samtools view -bS -F 4 -F 8 -F 256 -> ${bowtie2_name}_bowtie2.bam
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"""
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}
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37
tools/bowtie2/meta.yml
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tools/bowtie2/meta.yml
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name: Bowtie 2
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description: Ultrafast alignment to reference genome
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keywords:
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- Alignment
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- Short reads
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- FM Index
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tools:
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- fastqc:
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description: |
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Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads
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to long reference sequences. It is particularly good at aligning reads of about
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50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively
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long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep
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its memory footprint small: for the human genome, its memory footprint is typically
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around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
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homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
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documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
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input:
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-
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- sample_id:
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type: string
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description: Sample identifier
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- reads:
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type: file
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description: Input FastQ file, or pair of files
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output:
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-
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- report:
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type: file
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description: mapping statistics report
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pattern: *bowtie2_stats.txt
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- alignment:
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type: file
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description: alignment file in BAM format
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pattern: *bowtie2.bam
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authors:
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- @FelixKrueger
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31
tools/bowtie2/test/main.nf
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31
tools/bowtie2/test/main.nf
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#!/usr/bin/env nextflow
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nextflow.preview.dsl=2
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params.outdir = "."
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params.genome = ""
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params.bowtie2_args = ''
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// Bowtie2 arguments should be supplied in the following format to work:
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// --bowtie2_args="--score-min L,0,-0.8"
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params.verbose = false
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if (params.verbose){
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println ("[WORKFLOW] BOWTIE2 ARGS: " + params.bowtie2_args)
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}
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// for other genomes this needs to be handled somehow to return all possible genomes
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genomeValues = ["name" : params.genome]
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genomeValues["bowtie2"] = "/bi/home/fkrueger/VersionControl/nf-core-modules/test-datasets/indices/bowtie2/E_coli/${params.genome}";
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include '../main.nf' params(genome: genomeValues)
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ch_read_files = Channel
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.fromFilePairs('../../../test-datasets/Ecoli*{1,2}.fastq.gz',size:-1)
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// .view() // to check whether the input channel works
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workflow {
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main:
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BOWTIE2(ch_read_files, params.outdir, params.bowtie2_args, params.verbose)
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}
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2
tools/bowtie2/test/nextflow.config
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2
tools/bowtie2/test/nextflow.config
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docker.enabled = true
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params.outdir = './results'
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