process IVAR_VARIANTS { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0' : 'quay.io/biocontainers/ivar:1.3.1--h089eab3_0' }" input: tuple val(meta), path(bam) path fasta path gff output: tuple val(meta), path("*.tsv") , emit: tsv tuple val(meta), path("*.mpileup"), optional:true, emit: mpileup path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def save_mpileup = params.save_mpileup ? "tee ${prefix}.mpileup |" : "" def features = params.gff ? "-g $gff" : "" """ samtools mpileup \\ $args2 \\ --reference $fasta \\ $bam | \\ $save_mpileup \\ ivar variants \\ $args \\ $features \\ -r $fasta \\ -p $prefix cat <<-END_VERSIONS > versions.yml "${task.process}": ivar: \$(echo \$(ivar version 2>&1) | sed 's/^.*iVar version //; s/ .*\$//') END_VERSIONS """ }