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https://github.com/MillironX/nf-core_modules.git
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71 lines
2.5 KiB
Text
71 lines
2.5 KiB
Text
process BOWTIE2_ALIGN {
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tag "$meta.id"
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label "process_high"
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conda (params.enable_conda ? "bioconda::bowtie2=2.4.4 bioconda::samtools=1.15.1 conda-forge::pigz=2.6" : null)
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container "${ 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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input:
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tuple val(meta), path(reads)
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path index
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val save_unaligned
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val sort_bam
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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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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 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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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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unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ""
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reads_args = "-1 ${reads[0]} -2 ${reads[1]}"
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}
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def samtools_command = sort_bam ? 'sort' : 'view'
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"""
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INDEX=`find -L ./ -name "*.rev.1.bt2" | sed "s/.rev.1.bt2//"`
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[ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed "s/.rev.1.bt2l//"`
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[ -z "\$INDEX" ] && echo "Bowtie2 index files not found" 1>&2 && exit 1
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bowtie2 \\
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-x \$INDEX \\
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$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 $samtools_command $args2 --threads $task.cpus -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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}
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