process BCFTOOLS_MPILEUP { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' : 'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }" input: tuple val(meta), path(bam) path fasta output: tuple val(meta), path("*.gz") , emit: vcf tuple val(meta), path("*.tbi") , emit: tbi tuple val(meta), path("*stats.txt"), emit: stats path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' def args3 = task.ext.args3 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ echo "${meta.id}" > sample_name.list bcftools mpileup \\ --fasta-ref $fasta \\ $args \\ $bam \\ | bcftools call --output-type v $args2 \\ | bcftools reheader --samples sample_name.list \\ | bcftools view --output-file ${prefix}.vcf.gz --output-type z $args3 tabix -p vcf -f ${prefix}.vcf.gz bcftools stats ${prefix}.vcf.gz > ${prefix}.bcftools_stats.txt cat <<-END_VERSIONS > versions.yml "${task.process}": bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') END_VERSIONS """ }