process ADAPTERREMOVAL { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::adapterremoval=2.3.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/adapterremoval:2.3.2--hb7ba0dd_0' : 'quay.io/biocontainers/adapterremoval:2.3.2--hb7ba0dd_0' }" input: tuple val(meta), path(reads) path(adapterlist) output: tuple val(meta), path("${prefix}.truncated.gz") , optional: true, emit: singles_truncated tuple val(meta), path("${prefix}.discarded.gz") , optional: true, emit: discarded tuple val(meta), path("${prefix}.pair1.truncated.gz") , optional: true, emit: pair1_truncated tuple val(meta), path("${prefix}.pair2.truncated.gz") , optional: true, emit: pair2_truncated tuple val(meta), path("${prefix}.collapsed.gz") , optional: true, emit: collapsed tuple val(meta), path("${prefix}.collapsed.truncated.gz") , optional: true, emit: collapsed_truncated tuple val(meta), path("${prefix}.paired.gz") , optional: true, emit: paired_interleaved tuple val(meta), path('*.log') , emit: log path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' def list = adapterlist ? "--adapter-list ${adapterlist}" : "" prefix = task.ext.prefix ?: "${meta.id}" if (meta.single_end) { """ AdapterRemoval \\ --file1 $reads \\ $args \\ $adapterlist \\ --basename ${prefix} \\ --threads ${task.cpus} \\ --settings ${prefix}.log \\ --seed 42 \\ --gzip cat <<-END_VERSIONS > versions.yml "${task.process}": adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g") END_VERSIONS """ } else { """ AdapterRemoval \\ --file1 ${reads[0]} \\ --file2 ${reads[1]} \\ $args \\ $adapterlist \\ --basename ${prefix} \\ --threads $task.cpus \\ --settings ${prefix}.log \\ --seed 42 \\ --gzip cat <<-END_VERSIONS > versions.yml "${task.process}": adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g") END_VERSIONS """ } }