process SNAPALIGNER_ALIGN { tag '$meta.id' label 'process_high' conda (params.enable_conda ? "bioconda::snap-aligner=2.0.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/snap-aligner:2.0.1--hd03093a_1': 'quay.io/biocontainers/snap-aligner:2.0.1--hd03093a_1' }" input: tuple val(meta), path(reads) path index output: tuple val(meta), path("*.bam"), emit: bam path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def subcmd = meta.single_end ? "single" : "paired" """ mkdir -p index mv $index index/ snap-aligner ${subcmd} \\ index \\ ${reads.join(" ")} \\ -o ${prefix}.bam \\ -t ${task.cpus} \\ $args cat <<-END_VERSIONS > versions.yml "${task.process}": snapaligner: \$(snap-aligner 2>&1| head -n 1 | sed 's/^.*version //;s/.\$//') END_VERSIONS """ }