process ADAPTERREMOVALFIXPREFIX { tag "$meta.id" label 'process_medium' // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::adapterremovalfixprefix=0.0.5" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/adapterremovalfixprefix:0.0.5--hdfd78af_2': 'quay.io/biocontainers/adapterremovalfixprefix:0.0.5--hdfd78af_2' }" input: tuple val(meta), path(fastq) output: tuple val(meta), path("*.fq.gz"), emit: fixed_fastq path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" if ("$fastq" == "${prefix}.fq.gz") error "Input and output names are the same, set prefix in module configuration to disambiguate!" def VERSION = '0.0.5' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ AdapterRemovalFixPrefix \\ $fastq \\ $args \\ | gzip > ${prefix}.fq.gz cat <<-END_VERSIONS > versions.yml "${task.process}": adapterremovalfixprefix: $VERSION END_VERSIONS """ }