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47 lines
1.6 KiB
Text
47 lines
1.6 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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def VERSION = 0.1 // No version information printed
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process CHROMAP_INDEX {
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tag '$fasta'
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label 'process_medium'
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publishDir "${params.outdir}",
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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), meta:[:], publish_by_meta:[]) }
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conda (params.enable_conda ? "bioconda::chromap=0.1 bioconda::samtools=1.13" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:2cad7c5aa775241887eff8714259714a39baf016-0"
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} else {
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container "quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:2cad7c5aa775241887eff8714259714a39baf016-0"
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}
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input:
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path fasta
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output:
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path "*.index" , emit: index
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path "versions.yml", emit: version
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script:
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def software = getSoftwareName(task.process)
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def prefix = fasta.baseName
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"""
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chromap \\
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-i \\
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$options.args \\
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-t $task.cpus \\
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-r $fasta \\
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-o ${prefix}.index
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo "$VERSION")
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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END_VERSIONS
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"""
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}
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