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https://github.com/MillironX/nf-core_modules.git
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e751e5040a
* Bump software versions for viralrecon modules * Remove custom params.save_unaligned from bowtie2_align * Unify samtools modules and error if input and output names are the same * Fix ALL the tests
45 lines
1.4 KiB
Text
45 lines
1.4 KiB
Text
process BCFTOOLS_MPILEUP {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
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'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
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input:
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tuple val(meta), path(bam)
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path fasta
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output:
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tuple val(meta), path("*.gz") , emit: vcf
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tuple val(meta), path("*.tbi") , emit: tbi
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tuple val(meta), path("*stats.txt"), emit: stats
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path "versions.yml" , emit: versions
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script:
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def args = task.ext.args ?: ''
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def args2 = task.ext.args2 ?: ''
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def args3 = task.ext.args3 ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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echo "${meta.id}" > sample_name.list
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bcftools mpileup \\
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--fasta-ref $fasta \\
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$args \\
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$bam \\
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| bcftools call --output-type v $args2 \\
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| bcftools reheader --samples sample_name.list \\
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| bcftools view --output-file ${prefix}.vcf.gz --output-type z $args3
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tabix -p vcf -f ${prefix}.vcf.gz
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bcftools stats ${prefix}.vcf.gz > ${prefix}.bcftools_stats.txt
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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