process RSEQC_INFEREXPERIMENT { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : 'quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1' }" input: tuple val(meta), path(bam) path bed output: tuple val(meta), path("*.infer_experiment.txt"), emit: txt path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ infer_experiment.py \\ -i $bam \\ -r $bed \\ $args \\ > ${prefix}.infer_experiment.txt cat <<-END_VERSIONS > versions.yml "${task.process}": rseqc: \$(infer_experiment.py --version | sed -e "s/infer_experiment.py //g") END_VERSIONS """ }