process SAMTOOLS_CONVERT { tag "$meta.id" label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }" input: tuple val(meta), path(input), path(index) path fasta path fai output: tuple val(meta), path("*.{cram,bam}"), path("*.{crai,bai}") , emit: alignment_index 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 output_extension = input.getExtension() == "bam" ? "cram" : "bam" """ samtools view \\ --threads ${task.cpus} \\ --reference ${fasta} \\ $args \\ $input \\ -o ${prefix}.${output_extension} samtools index -@${task.cpus} ${prefix}.${output_extension} cat <<-END_VERSIONS > versions.yml "${task.process}": samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ }