2021-02-17 17:23:11 +00:00
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// Import generic module functions
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2021-09-27 08:41:24 +00:00
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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2021-02-17 17:23:11 +00:00
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params.options = [:]
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2021-03-15 12:16:43 +00:00
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options = initOptions(params.options)
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2021-02-17 17:23:11 +00:00
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process BWAMETH_ALIGN {
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tag "$meta.id"
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label 'process_high'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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2021-04-09 16:23:56 +00:00
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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2021-02-17 17:23:11 +00:00
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conda (params.enable_conda ? "bioconda::bwameth=0.2.2" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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2021-04-06 09:45:14 +00:00
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container "https://depot.galaxyproject.org/singularity/bwameth:0.2.2--py_1"
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2021-02-17 17:23:11 +00:00
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} else {
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2021-04-06 09:45:14 +00:00
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container "quay.io/biocontainers/bwameth:0.2.2--py_1"
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2021-02-17 17:23:11 +00:00
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}
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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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2021-10-01 13:04:56 +00:00
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path "versions.yml" , emit: versions
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2021-02-17 17:23:11 +00:00
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
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"""
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2021-02-20 12:12:43 +00:00
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INDEX=`find -L ${index} -name "*.bwameth.c2t" | sed 's/.bwameth.c2t//'`
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2021-02-20 11:51:01 +00:00
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2021-11-06 15:05:04 +00:00
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# Modify the timestamps so that bwameth doesn't complain about building the index
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# See https://github.com/nf-core/methylseq/pull/217
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touch -c -- *
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2021-02-17 17:23:11 +00:00
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bwameth.py \\
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$options.args \\
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$read_group \\
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2021-09-30 08:26:52 +00:00
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-t $task.cpus \\
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2021-02-20 11:51:01 +00:00
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--reference \$INDEX \\
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2021-02-17 17:23:11 +00:00
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$reads \\
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2021-09-30 08:26:52 +00:00
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| samtools view $options.args2 -@ $task.cpus -bhS -o ${prefix}.bam -
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2021-02-17 17:23:11 +00:00
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2021-09-27 08:41:24 +00:00
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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2021-09-27 21:10:37 +00:00
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${getSoftwareName(task.process)}: \$(echo \$(bwameth.py --version 2>&1) | cut -f2 -d" ")
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2021-09-27 08:41:24 +00:00
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END_VERSIONS
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2021-02-17 17:23:11 +00:00
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"""
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}
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