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90aef30f43
* Set process label to `process_single` for modules with no `task.cpus` usage * Fix tests of 'borked' modules * prettier * More modules are single-threaded and can use process_single * Adding process_single to hmmer/esl* modules * Fix failing tests * Prettier Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk> Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
72 lines
2.7 KiB
Text
72 lines
2.7 KiB
Text
process MULTIVCFANALYZER {
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tag '$fasta'
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label 'process_single'
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conda (params.enable_conda ? "bioconda::multivcfanalyzer=0.85.2" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/multivcfanalyzer:0.85.2--hdfd78af_1':
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'quay.io/biocontainers/multivcfanalyzer:0.85.2--hdfd78af_1' }"
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input:
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path vcfs
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path fasta
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path snpeff_results
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path gff
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val allele_freqs
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val genotype_quality
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val coverage
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val homozygous_freq
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val heterozygous_freq
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path gff_exclude
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output:
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path('fullAlignment.fasta.gz') , emit: full_alignment
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path('info.txt') , emit: info_txt
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path('snpAlignment.fasta.gz') , emit: snp_alignment
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path('snpAlignmentIncludingRefGenome.fasta.gz') , emit: snp_genome_alignment
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path('snpStatistics.tsv') , emit: snpstatistics
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path('snpTable.tsv') , emit: snptable
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path('snpTableForSnpEff.tsv') , emit: snptable_snpeff
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path('snpTableWithUncertaintyCalls.tsv') , emit: snptable_uncertainty
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path('structureGenotypes.tsv') , emit: structure_genotypes
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path('structureGenotypes_noMissingData-Columns.tsv') , emit: structure_genotypes_nomissing
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path('MultiVCFAnalyzer.json') , emit: json
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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// def args = task.ext.args ?: '' // MultiVCFAnalyzer has strict and input ordering and all are mandatory. Deactivating $args to prevent breakage of input
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def args2 = task.ext.args2 ?: ''
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def cmd_snpeff_results = snpeff_results ? "${snpeff_results}" : "NA"
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def cmd_gff = gff ? "${gff}" : "NA"
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def cmd_allele_freqs = allele_freqs ? "T" : "F"
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def cmd_gff_exclude = gff_exclude ? "${gff}" : "NA"
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"""
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multivcfanalyzer \\
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${cmd_snpeff_results} \\
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${fasta} \\
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${cmd_gff} \\
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. \
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${cmd_allele_freqs} \\
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${genotype_quality} \\
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${coverage} \\
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${homozygous_freq} \\
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${heterozygous_freq} \\
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${cmd_gff_exclude} \\
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${vcfs.join(" ")}
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gzip \\
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$args2 \\
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fullAlignment.fasta snpAlignment.fasta snpAlignmentIncludingRefGenome.fasta
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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multivcfanalyzer: \$(echo \$(multivcfanalyzer --help | head -n 1) | cut -f 3 -d ' ' )
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END_VERSIONS
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"""
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}
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