process YARA_MAPPER { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::yara=1.0.2 bioconda::samtools=1.15.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:d6c969c1e20cc02a9234961c07a24bb0887f05ea-0' : 'quay.io/biocontainers/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:d6c969c1e20cc02a9234961c07a24bb0887f05ea-0' }" input: tuple val(meta), path(reads) path index output: tuple val(meta), path("*.mapped.bam"), emit: bam tuple val(meta), path("*.mapped.bam.bai"), emit: bai 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}" if (meta.single_end) { """ yara_mapper \\ $args \\ -t $task.cpus \\ -f bam \\ ${index}/yara \\ $reads | samtools view -@ $task.cpus -hb -F4 | samtools sort -@ $task.cpus > ${prefix}.mapped.bam samtools index -@ $task.cpus ${prefix}.mapped.bam cat <<-END_VERSIONS > versions.yml "${task.process}": yara: \$(echo \$(yara_mapper --version 2>&1) | sed 's/^.*yara_mapper version: //; s/ .*\$//') samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ } else { """ yara_mapper \\ $args \\ -t $task.cpus \\ -f bam \\ ${index}/yara \\ ${reads[0]} \\ ${reads[1]} > output.bam samtools view -@ $task.cpus -hF 4 -f 0x40 -b output.bam | samtools sort -@ $task.cpus > ${prefix}_1.mapped.bam samtools view -@ $task.cpus -hF 4 -f 0x80 -b output.bam | samtools sort -@ $task.cpus > ${prefix}_2.mapped.bam samtools index -@ $task.cpus ${prefix}_1.mapped.bam samtools index -@ $task.cpus ${prefix}_2.mapped.bam cat <<-END_VERSIONS > versions.yml "${task.process}": yara: \$(echo \$(yara_mapper --version 2>&1) | sed 's/^.*yara_mapper version: //; s/ .*\$//') samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ } }