process HISAT2_EXTRACTSPLICESITES { tag "$gtf" label 'process_medium' // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? 'bioconda::hisat2=2.2.1' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hisat2:2.2.1--h1b792b2_3' : 'quay.io/biocontainers/hisat2:2.2.1--h1b792b2_3' }" input: path gtf output: path "*.splice_sites.txt", emit: txt path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' def VERSION = '2.2.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ hisat2_extract_splice_sites.py $gtf > ${gtf.baseName}.splice_sites.txt cat <<-END_VERSIONS > versions.yml "${task.process}": hisat2: $VERSION END_VERSIONS """ }