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46 lines
1.4 KiB
Text
46 lines
1.4 KiB
Text
process BWAMETH_ALIGN {
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tag "$meta.id"
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label 'process_high'
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conda (params.enable_conda ? "bioconda::bwameth=0.2.2" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bwameth:0.2.2--py_1' :
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'quay.io/biocontainers/bwameth:0.2.2--py_1' }"
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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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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 read_group = meta.read_group ? "-R ${meta.read_group}" : ""
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"""
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INDEX=`find -L ${index} -name "*.bwameth.c2t" | sed 's/.bwameth.c2t//'`
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# Modify the timestamps so that bwameth doesn't complain about building the index
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# See https://github.com/nf-core/methylseq/pull/217
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touch -c -- *
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bwameth.py \\
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$args \\
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$read_group \\
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-t $task.cpus \\
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--reference \$INDEX \\
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$reads \\
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| samtools view $args2 -@ $task.cpus -bhS -o ${prefix}.bam -
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bwameth: \$(echo \$(bwameth.py --version 2>&1) | cut -f2 -d" ")
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END_VERSIONS
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"""
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}
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