nf-core_modules/software/hisat2/extractsplicesites/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
options = initOptions(params.options)
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def VERSION = '2.2.0'
process HISAT2_EXTRACTSPLICESITES {
tag "$gtf"
label 'process_medium'
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publishDir "${params.outdir}",
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)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/hisat2:2.2.0--py37hfa133b6_4"
} else {
container "quay.io/biocontainers/hisat2:2.2.0--py37hfa133b6_4"
}
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input:
path gtf
output:
path "*.splice_sites.txt", emit: txt
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
"""
hisat2_extract_splice_sites.py $gtf > ${gtf.baseName}.splice_sites.txt
echo $VERSION > ${software}.version.txt
"""
}