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74ff11b07b
* Fix bowtie build test * Forgot to delete old bowtie_build * Fix bowtie2 build tests * Add initOptions include on hisat2 extractsplicesites
35 lines
1.1 KiB
Text
35 lines
1.1 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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def VERSION = '2.2.0'
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process HISAT2_EXTRACTSPLICESITES {
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tag "$gtf"
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publishDir "${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), publish_id:'') }
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conda (params.enable_conda ? "bioconda::hisat2=2.2.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/hisat2:2.2.0--py37hfa133b6_4"
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} else {
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container "quay.io/biocontainers/hisat2:2.2.0--py37hfa133b6_4"
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}
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input:
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path gtf
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output:
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path "*.splice_sites.txt", emit: txt
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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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hisat2_extract_splice_sites.py $gtf > ${gtf.baseName}.splice_sites.txt
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echo $VERSION > ${software}.version.txt
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"""
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}
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