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67c1bc9568
* callcnvs stub and tests * partition stub and test * histogram stub and test * importreaddepth stub and tests * update module scripts Co-authored-by: Sima Rahimi <sima.rahimi@gu.se>
44 lines
1.2 KiB
Text
44 lines
1.2 KiB
Text
process CNVPYTOR_CALLCNVS {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::cnvpytor=1.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/cnvpytor:1.0--py39h6a678da_2':
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'quay.io/biocontainers/cnvpytor:1.0--py39h6a678da_2' }"
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input:
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tuple val(meta), path(pytor)
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output:
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tuple val(meta), path("*.tsv"), emit: cnvs
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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 ?: '1000'
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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cnvpytor \\
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-root $pytor \\
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-call $args > ${prefix}.tsv
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
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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 ${prefix}.tsv
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
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END_VERSIONS
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"""
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}
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