def VERSION = '1.2.15' // Version information not provided by tool on CLI process LEEHOM { tag "$meta.id" label 'process_low' conda (params.enable_conda ? "bioconda::leehom=1.2.15" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/leehom:1.2.15--h29e30f7_1' : 'quay.io/biocontainers/leehom:1.2.15--h29e30f7_1' }" input: tuple val(meta), path(reads) output: tuple val(meta), path("${prefix}.bam") , optional: true, emit: bam tuple val(meta), path("${prefix}.fq.gz") , optional: true, emit: fq_pass tuple val(meta), path("${prefix}.fail.fq.gz") , optional: true, emit: fq_fail tuple val(meta), path("${prefix}_r1.fq.gz") , optional: true, emit: unmerged_r1_fq_pass tuple val(meta), path("${prefix}_r1.fail.fq.gz"), optional: true, emit: unmerged_r1_fq_fail tuple val(meta), path("${prefix}_r2.fq.gz") , optional: true, emit: unmerged_r2_fq_pass tuple val(meta), path("${prefix}_r2.fail.fq.gz"), optional: true, emit: unmerged_r2_fq_fail tuple val(meta), path("*.log") , emit: log path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" if (reads.toString().endsWith('.bam')) { """ leeHom \\ $args \\ -t $task.cpus \\ -o ${prefix}.bam \\ --log ${prefix}.log \\ $reads cat <<-END_VERSIONS > versions.yml "${task.process}": leehom: $VERSION END_VERSIONS """ } else if (meta.single_end) { """ leeHom \\ $args \\ -t $task.cpus \\ -fq1 $reads \\ -fqo $prefix \\ --log ${prefix}.log cat <<-END_VERSIONS > versions.yml "${task.process}": leehom: $VERSION END_VERSIONS """ } else { """ leeHom \\ $args \\ -t $task.cpus \\ -fq1 ${reads[0]} \\ -fq2 ${reads[1]} \\ -fqo $prefix \\ --log ${prefix}.log cat <<-END_VERSIONS > versions.yml "${task.process}": leehom: $VERSION END_VERSIONS """ } }