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https://github.com/MillironX/nf-core_modules.git
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58 lines
2.2 KiB
Text
58 lines
2.2 KiB
Text
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process BISCUIT_EPIREAD {
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tag "$meta.id"
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label 'process_long'
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conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0':
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'quay.io/biocontainers/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0' }"
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input:
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tuple val(meta), path(bam), path(bai), path(snp_bed)
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path(index)
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output:
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tuple val(meta), path("*.bed.gz"), emit: epiread_bed
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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 ?: "${meta.id}"
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def biscuit_cpus = (int) Math.max(Math.floor(task.cpus*0.9),1)
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def samtools_cpus = task.cpus-biscuit_cpus
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// As of 2/25/22, epiread does not support reading a gzipped SNP BED file.
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// This is a bit hacky but allows the user to supply a gzipped OR uncompressed bed file
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def unzip_snp_bed = snp_bed && (snp_bed.toString() =~ /\.gz$/) ? "bgzip -d ${snp_bed}" : ""
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def unzipped_snp_bed = snp_bed ? snp_bed.toString() - ~/\.gz$/: ""
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// SNP BED input is optional
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def options_snp_bed = snp_bed ? "-B ${unzipped_snp_bed}" : ""
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if ("$options_snp_bed" == "${prefix}.bed.gz") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
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"""
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INDEX=`find -L ./ -name "*.bis.amb" | sed 's/.bis.amb//'`
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$unzip_snp_bed
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biscuit epiread \\
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-@ $biscuit_cpus \\
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$args \\
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$options_snp_bed \\
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\$INDEX \\
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$bam | \\
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LC_ALL=C sort -k1,1 -k2,2n | \\
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bgzip \\
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-@ $samtools_cpus \\
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$args2 \\
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-c > ${prefix}.bed.gz
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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biscuit: \$( biscuit version |& sed '1!d; s/^.*BISCUIT Version: //' )
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samtools: \$( samtools --version |& sed '1!d; s/^.*samtools //' )
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END_VERSIONS
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"""
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}
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