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57 lines
2 KiB
Text
57 lines
2 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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def options = initOptions(params.options)
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process IVAR_CONSENSUS {
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tag "$meta.id"
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label 'process_medium'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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conda (params.enable_conda ? "bioconda::ivar=1.3.1=h089eab3_0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0"
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} else {
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container "quay.io/biocontainers/ivar:1.3.1--h089eab3_0"
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}
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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("*.fa") , emit: fasta
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tuple val(meta), path("*.qual.txt"), emit: qual
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tuple val(meta), path("*.mpileup") , emit: mpileup
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def save_mpileup = options.save_mpileup ? "tee ${prefix}.mpileup |" : ""
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def min_bq = options.min_bq ? "-Q ${options.min_bq}" : "-Q 0"
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def max_depth = options.max_depth ? "-d ${options.max_depth}" : "-d 0"
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def count_orphans = options.count_orphans ? "-A" : ""
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def disable_baq = options.disable_baq ? "-B" : ""
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def output_all_bases = options.output_all_bases ? "-aa" : ""
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"""
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samtools mpileup \\
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--fasta-ref $fasta \\
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$output_all_bases \\
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$count_orphans \\
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$disable_baq \\
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$max_depth \\
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$min_bq \\
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$options.args2 \\
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$bam | \\
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$save_mpileup \\
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ivar consensus \\
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$options.args \\
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-p $prefix
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ivar version | head -n1 2>&1 | sed 's/^.*iVar version //g' > ${software}.version.txt
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"""
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}
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