mirror of
https://github.com/MillironX/nf-core_modules.git
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54 lines
1.4 KiB
Text
54 lines
1.4 KiB
Text
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def VERSION_HAP = '0.3.14'
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def VERSION_PRE = '0.3.14'
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process HAPPY {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::hap.py=0.3.14" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/hap.py:0.3.14--py27h5c5a3ab_0':
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'quay.io/biocontainers/hap.py:0.3.14--py27h5c5a3ab_0' }"
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input:
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tuple val(meta), path(truth_vcf), path(query_vcf), path(bed)
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tuple path(fasta), path(fasta_fai)
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output:
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tuple val(meta), path('*.csv'), path('*.json') , emit: metrics
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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 ?: ''
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def args2 = task.ext.args2 ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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pre.py \\
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$args \\
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-R $bed \\
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--reference $fasta \\
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--threads $task.cpus \\
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$query_vcf \\
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${prefix}_preprocessed.vcf.gz
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hap.py \\
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$truth_vcf \\
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${prefix}_preprocessed.vcf.gz \\
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$args2 \\
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--reference $fasta \\
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--threads $task.cpus \\
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-R $bed \\
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-o $prefix
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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hap.py: $VERSION_HAP
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pre.py: $VERSION_PRE
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END_VERSIONS
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"""
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}
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