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seacr | PR review changes
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1 changed files with 5 additions and 4 deletions
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@ -4,6 +4,8 @@ include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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params.options = [:]
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def options = initOptions(params.options)
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def options = initOptions(params.options)
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def VERSION = '1.3'
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process SEACR_CALLPEAK {
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process SEACR_CALLPEAK {
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tag "$meta.id"
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tag "$meta.id"
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label 'process_medium'
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label 'process_medium'
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@ -11,8 +13,7 @@ process SEACR_CALLPEAK {
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mode: params.publish_dir_mode,
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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conda (params.enable_conda ? "bioconda::seacr=1.3" : null)
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conda (params.enable_conda ? "bioconda::seacr=1.3 conda-forge::r-base=4.0.2 bioconda::bedtools=2.29.2" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:5bb5ed4307a8187a7f34730b00431de93688fa59-0"
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container "https://depot.galaxyproject.org/singularity/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:5bb5ed4307a8187a7f34730b00431de93688fa59-0"
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} else {
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} else {
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@ -36,6 +37,6 @@ process SEACR_CALLPEAK {
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$options.args \\
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$options.args \\
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$prefix
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$prefix
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echo 1.3 > ${software}.version.txt
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echo $VERSION > ${software}.version.txt
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"""
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"""
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}
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}
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