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6a46e7cf11
* Allow to pass arguments to the script itself * Place args2 correctly * Define args2 aaaaarrrrgggg * Testing locally before commiting is a good practice * Update modules/phantompeakqualtools/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
37 lines
1.2 KiB
Text
37 lines
1.2 KiB
Text
def VERSION = '1.2.2' // Version information not provided by tool on CLI
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process PHANTOMPEAKQUALTOOLS {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::phantompeakqualtools=1.2.2" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/phantompeakqualtools:1.2.2--0' :
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'quay.io/biocontainers/phantompeakqualtools:1.2.2--0' }"
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input:
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tuple val(meta), path(bam)
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output:
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tuple val(meta), path("*.out") , emit: spp
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tuple val(meta), path("*.pdf") , emit: pdf
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tuple val(meta), path("*.Rdata"), emit: rdata
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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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"""
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RUN_SPP=`which run_spp.R`
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Rscript $args -e "library(caTools); source(\\"\$RUN_SPP\\")" -c="$bam" -savp="${prefix}.spp.pdf" -savd="${prefix}.spp.Rdata" -out="${prefix}.spp.out" $args2
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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phantompeakqualtools: $VERSION
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END_VERSIONS
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"""
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}
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