include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) process LOFREQ_INDELQUAL { tag "$meta.id" label 'process_low' publishDir "${params.outdir}", mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { container "https://depot.galaxyproject.org/singularity/lofreq:2.1.5--py38h588ecb2_4" } else { container "quay.io/biocontainers/lofreq:2.1.5--py38h588ecb2_4" } input: tuple val(meta), path(bam) path fasta output: tuple val(meta), path("*.bam"), emit: bam path "versions.yml" , emit: versions script: def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ lofreq indelqual \\ $options.args \\ -f $fasta \\ -o ${prefix}.bam \\ $bam cat <<-END_VERSIONS > versions.yml ${getProcessName(task.process)}: ${getSoftwareName(task.process)}: \$(echo \$(lofreq version 2>&1) | sed 's/^version: //; s/ *commit.*\$//') END_VERSIONS """ }