mirror of
https://github.com/MillironX/nf-core_modules.git
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9ae34a01d1
* Fix typo * Add stub runs for testing input without matched normals * Add missing -stub-run * remove empty file checksum tests and change workflow names * test controlfreec naming * fix output file names * fix output file names * fix output file names * fix conda and container path difference for R scripts * update tar version to work with conda * fix version number in docker * try to fix path to script, pretty sure it won't work * try new ways to set path with wildcard * try which * add which but with escape * remove comment
52 lines
1.7 KiB
Text
52 lines
1.7 KiB
Text
process CONTROLFREEC_MAKEGRAPH {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::control-freec=11.6" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1':
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'quay.io/biocontainers/control-freec:11.6--h1b792b2_1' }"
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input:
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tuple val(meta), path(ratio), path(baf)
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output:
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tuple val(meta), path("*_BAF.png") , emit: png_baf
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tuple val(meta), path("*_ratio.log2.png"), emit: png_ratio_log2
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tuple val(meta), path("*_ratio.png") , emit: png_ratio
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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 baf = baf ?: ""
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"""
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cat \$(which makeGraph.R) | R --slave --args ${args} ${ratio} ${baf}
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mv *_BAF.txt.png ${prefix}_BAF.png
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mv *_ratio.txt.log2.png ${prefix}_ratio.log2.png
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mv *_ratio.txt.png ${prefix}_ratio.png
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
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END_VERSIONS
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"""
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch ${prefix}_BAF.png
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touch ${prefix}_ratio.log2.png
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touch ${prefix}_ratio.png
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
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END_VERSIONS
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"""
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}
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