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39 lines
1.2 KiB
Text
39 lines
1.2 KiB
Text
process BISMARK_ALIGN {
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tag "$meta.id"
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label 'process_high'
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conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' :
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'quay.io/biocontainers/bismark:0.23.0--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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output:
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tuple val(meta), path("*bam") , emit: bam
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tuple val(meta), path("*report.txt"), emit: report
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tuple val(meta), path("*fq.gz") , optional:true, emit: unmapped
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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 prefix = task.ext.prefix ?: "${meta.id}"
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def fastq = meta.single_end ? reads : "-1 ${reads[0]} -2 ${reads[1]}"
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"""
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bismark \\
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$fastq \\
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$args \\
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--genome $index \\
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--bam
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
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END_VERSIONS
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"""
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}
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