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217303f5c1
* Add option -p to set the # of cpus on stringtie * Bump version 2.1.7 to stringtie modules * Output stringtie/merge version * Fix padding * Apply suggestions from code review * Defining software variable * Fix test, gff can't be md5 check, contains instead Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
39 lines
1.3 KiB
Text
39 lines
1.3 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process STRINGTIE_MERGE {
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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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// Note: 2.7X indices incompatible with AWS iGenomes.
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conda (params.enable_conda ? "bioconda::stringtie=2.1.7" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/stringtie:2.1.7--h978d192_0"
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} else {
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container "quay.io/biocontainers/stringtie:2.1.7--h978d192_0"
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}
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input:
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path stringtie_gtf
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path annotation_gtf
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output:
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path "stringtie.merged.gtf", emit: gtf
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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"""
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stringtie \\
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--merge $stringtie_gtf \\
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-G $annotation_gtf \\
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-o stringtie.merged.gtf
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echo \$(stringtie --version 2>&1) > ${software}.version.txt
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"""
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}
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