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https://github.com/MillironX/nf-core_modules.git
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Merge pull request #1645 from matthdsm/update/bowtie2-align
bowtie2: remove code duplication
This commit is contained in:
Matthias De Smet
GitHub
commit
1dccf12077
2 changed files with 62 additions and 133 deletions
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@ -1,11 +1,11 @@
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process BOWTIE2_ALIGN {
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tag "$meta.id"
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label 'process_high'
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label "process_high"
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conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4 bioconda::samtools=1.15.1 conda-forge::pigz=2.6' : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0' :
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'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0' }"
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conda (params.enable_conda ? "bioconda::bowtie2=2.4.4 bioconda::samtools=1.15.1 conda-forge::pigz=2.6" : null)
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container "${ workflow.containerEngine == "singularity" && !task.ext.singularity_pull_docker_container ?
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"https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0" :
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"quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0" }"
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input:
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tuple val(meta), path(reads)
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@ -13,69 +13,60 @@ process BOWTIE2_ALIGN {
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val save_unaligned
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output:
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tuple val(meta), path('*.bam') , emit: bam
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tuple val(meta), path('*.log') , emit: log
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tuple val(meta), path('*fastq.gz'), emit: fastq, optional:true
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tuple val(meta), path("*.bam") , emit: bam
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tuple val(meta), path("*.log") , emit: log
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tuple val(meta), path("*fastq.gz"), emit: fastq, optional:true
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def args2 = task.ext.args2 ?: ''
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def args = task.ext.args ?: ""
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def args2 = task.ext.args2 ?: ""
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def prefix = task.ext.prefix ?: "${meta.id}"
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def unaligned = ""
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def reads_args = ""
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if (meta.single_end) {
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def unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
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"""
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INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
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[ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed 's/.rev.1.bt2l//'`
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[ -z "\$INDEX" ] && echo "BT2 index files not found" 1>&2 && exit 1
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bowtie2 \\
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-x \$INDEX \\
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-U $reads \\
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--threads $task.cpus \\
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$unaligned \\
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$args \\
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2> ${prefix}.bowtie2.log \\
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| samtools view -@ $task.cpus $args2 -bhS -o ${prefix}.bam -
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
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END_VERSIONS
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"""
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unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ""
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reads_args = "-U ${reads}"
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} else {
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def unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
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"""
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INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
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[ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed 's/.rev.1.bt2l//'`
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[ -z "\$INDEX" ] && echo "BT2 index files not found" 1>&2 && exit 1
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bowtie2 \\
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-x \$INDEX \\
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-1 ${reads[0]} \\
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-2 ${reads[1]} \\
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--threads $task.cpus \\
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$unaligned \\
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$args \\
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2> ${prefix}.bowtie2.log \\
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| samtools view -@ $task.cpus $args2 -bhS -o ${prefix}.bam -
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if [ -f ${prefix}.unmapped.fastq.1.gz ]; then
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mv ${prefix}.unmapped.fastq.1.gz ${prefix}.unmapped_1.fastq.gz
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fi
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if [ -f ${prefix}.unmapped.fastq.2.gz ]; then
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mv ${prefix}.unmapped.fastq.2.gz ${prefix}.unmapped_2.fastq.gz
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fi
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
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END_VERSIONS
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"""
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unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ""
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reads_args = "-1 ${reads[0]} -2 ${reads[1]}"
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}
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def samtools_command = "samtools view -@ $task.cpus --bam --with-header ${args2} > ${prefix}.bam"
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"""
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INDEX=`find -L ./ -name "*.rev.1.bt2" | sed "s/.rev.1.bt2//"`
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[ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed "s/.rev.1.bt2l//"`
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[ -z "\$INDEX" ] && echo "Bowtie2 index files not found" 1>&2 && exit 1
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bowtie2 \\
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-x \$INDEX \\
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$reads_args \\
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--threads $task.cpus \\
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$unaligned \\
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$args \\
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2> ${prefix}.bowtie2.log \\
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| $samtools_command
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if [ -f ${prefix}.unmapped.fastq.1.gz ]; then
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mv ${prefix}.unmapped.fastq.1.gz ${prefix}.unmapped_1.fastq.gz
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fi
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if [ -f ${prefix}.unmapped.fastq.2.gz ]; then
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mv ${prefix}.unmapped.fastq.2.gz ${prefix}.unmapped_2.fastq.gz
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fi
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
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END_VERSIONS
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"""
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}
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@ -1,83 +1,21 @@
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- name: bowtie2 align single-end
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- name: bowtie2 align test_bowtie2_align_single_end
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command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config
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tags:
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- bowtie2
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- bowtie2/align
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- bowtie2
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files:
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- path: ./output/bowtie2/test.bam
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- path: ./output/bowtie2/test.bowtie2.log
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- path: ./output/bowtie2/bowtie2/genome.3.bt2
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md5sum: 4ed93abba181d8dfab2e303e33114777
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- path: ./output/bowtie2/bowtie2/genome.2.bt2
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md5sum: 47b153cd1319abc88dda532462651fcf
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- path: ./output/bowtie2/bowtie2/genome.1.bt2
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md5sum: cbe3d0bbea55bc57c99b4bfa25b5fbdf
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- path: ./output/bowtie2/bowtie2/genome.4.bt2
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md5sum: c25be5f8b0378abf7a58c8a880b87626
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- path: ./output/bowtie2/bowtie2/genome.rev.1.bt2
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md5sum: 52be6950579598a990570fbcf5372184
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- path: ./output/bowtie2/bowtie2/genome.rev.2.bt2
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md5sum: e3b4ef343dea4dd571642010a7d09597
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- path: output/bowtie2/test.bam
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- path: output/bowtie2/test.bowtie2.log
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md5sum: 7b8a9e61b7646da1089b041333c41a87
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- path: output/bowtie2/versions.yml
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- name: bowtie2 align paired-end
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- name: bowtie2 align test_bowtie2_align_paired_end
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command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config
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tags:
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- bowtie2
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- bowtie2/align
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files:
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- path: ./output/bowtie2/test.bam
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- path: ./output/bowtie2/test.bowtie2.log
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- path: ./output/bowtie2/bowtie2/genome.3.bt2
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md5sum: 4ed93abba181d8dfab2e303e33114777
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- path: ./output/bowtie2/bowtie2/genome.2.bt2
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md5sum: 47b153cd1319abc88dda532462651fcf
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- path: ./output/bowtie2/bowtie2/genome.1.bt2
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md5sum: cbe3d0bbea55bc57c99b4bfa25b5fbdf
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- path: ./output/bowtie2/bowtie2/genome.4.bt2
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md5sum: c25be5f8b0378abf7a58c8a880b87626
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- path: ./output/bowtie2/bowtie2/genome.rev.1.bt2
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md5sum: 52be6950579598a990570fbcf5372184
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- path: ./output/bowtie2/bowtie2/genome.rev.2.bt2
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md5sum: e3b4ef343dea4dd571642010a7d09597
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- name: bowtie2 align single-end large-index
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command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config --force_large_index
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tags:
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- bowtie2
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- bowtie2/align
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files:
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- path: ./output/bowtie2/test.bam
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- path: ./output/bowtie2/test.bowtie2.log
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- path: ./output/bowtie2/bowtie2/genome.3.bt2l
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md5sum: 8952b3e0b1ce9a7a5916f2e147180853
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- path: ./output/bowtie2/bowtie2/genome.2.bt2l
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md5sum: 22c284084784a0720989595e0c9461fd
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- path: ./output/bowtie2/bowtie2/genome.1.bt2l
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md5sum: 07d811cd4e350d56267183d2ac7023a5
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- path: ./output/bowtie2/bowtie2/genome.4.bt2l
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md5sum: c25be5f8b0378abf7a58c8a880b87626
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- path: ./output/bowtie2/bowtie2/genome.rev.1.bt2l
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md5sum: fda48e35925fb24d1c0785f021981e25
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- path: ./output/bowtie2/bowtie2/genome.rev.2.bt2l
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md5sum: 802c26d32b970e1b105032b7ce7348b4
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- name: bowtie2 align paired-end large-index
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command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config --force_large_index
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tags:
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- bowtie2
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- bowtie2/align
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files:
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- path: ./output/bowtie2/test.bam
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- path: ./output/bowtie2/test.bowtie2.log
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- path: ./output/bowtie2/bowtie2/genome.3.bt2l
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md5sum: 8952b3e0b1ce9a7a5916f2e147180853
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- path: ./output/bowtie2/bowtie2/genome.2.bt2l
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md5sum: 22c284084784a0720989595e0c9461fd
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- path: ./output/bowtie2/bowtie2/genome.1.bt2l
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md5sum: 07d811cd4e350d56267183d2ac7023a5
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- path: ./output/bowtie2/bowtie2/genome.4.bt2l
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md5sum: c25be5f8b0378abf7a58c8a880b87626
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- path: ./output/bowtie2/bowtie2/genome.rev.1.bt2l
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md5sum: fda48e35925fb24d1c0785f021981e25
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- path: ./output/bowtie2/bowtie2/genome.rev.2.bt2l
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md5sum: 802c26d32b970e1b105032b7ce7348b4
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- path: output/bowtie2/test.bam
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- path: output/bowtie2/test.bowtie2.log
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md5sum: bd89ce1b28c93bf822bae391ffcedd19
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- path: output/bowtie2/versions.yml
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