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2f1555bf77
* feat(pints): Add initial caller module * docs(pints): Add initial documentation * chore: Add TODOs * test(pypints): Use docker image for singularity The image doesn't exist yet for some reason * test(pints): Remove unidirectional peaks hash * style(pints): Align emits
43 lines
1.5 KiB
Text
43 lines
1.5 KiB
Text
process PINTS_CALLER {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::pypints=1.1.6" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/pypints:1.1.6--pyh5e36f6f_1' :
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'quay.io/biocontainers/pypints:1.1.6--pyh5e36f6f_1' }"
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input:
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tuple val(meta), path(bams)
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output:
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tuple val(meta), path("*_divergent_peaks.bed") , emit: divergent_TREs
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tuple val(meta), path("*_bidirectional_peaks.bed") , emit: bidirectional_TREs
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tuple val(meta), path("*_unidirectional_peaks.bed"), emit: unidirectional_TREs
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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 ?: "${meta.id}"
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// TODO handle bigwigs
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// def input_type = ("${input[0]}".endsWith(".bam")) ? "--bam-file $input" :
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// ("$input".contains(".bw")) ? "--bw-pl ${input[0]} --bw-mn ${input[1]}" :
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// error "Please use bam or BigWig files"
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"""
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pints_caller \\
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--bam-file $bams \\
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--save-to . \\
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--file-prefix $prefix \\
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--thread $task.cpus \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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python: \$(python --version | sed 's/Python //g')
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pints: \$(pints_caller --version)
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END_VERSIONS
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"""
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}
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