process ISMAPPER { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::ismapper=2.0.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ismapper:2.0.2--pyhdfd78af_1' : 'quay.io/biocontainers/ismapper:2.0.2--pyhdfd78af_1' }" input: tuple val(meta), path(reads), path(reference), path(query) output: tuple val(meta), path("results/*"), emit: results path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ ismap \\ $args \\ --t $task.cpus \\ --output_dir results \\ --queries $query \\ --reference $reference \\ --reads $reads cat <<-END_VERSIONS > versions.yml "${task.process}": ismapper: \$( echo \$( ismap --version 2>&1 ) | sed 's/^.*ismap //' ) END_VERSIONS """ }