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67 lines
2.3 KiB
Text
67 lines
2.3 KiB
Text
process DEEPTOOLS_BAMCOVERAGE {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::deeptools=3.5.1 bioconda::samtools=1.15.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:2c687053c0252667cca265c9f4118f2c205a604c-0':
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'quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:2c687053c0252667cca265c9f4118f2c205a604c-0' }"
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input:
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tuple val(meta), path(input), path(input_index)
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path(fasta)
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path(fasta_fai)
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output:
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tuple val(meta), path("*.bigWig") , emit: bigwig, optional: true
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tuple val(meta), path("*.bedgraph") , emit: bedgraph, optional: true
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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 prefix = task.ext.prefix ?: "${meta.id}.bigWig"
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// cram_input is currently not working with deeptools
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// therefore it's required to convert cram to bam first
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def is_cram = input.Extension == "cram" ? true : false
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def input_out = is_cram ? input.BaseName + ".bam" : "${input}"
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def fai_reference = fasta_fai ? "--fai-reference ${fasta_fai}" : ""
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if (is_cram){
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"""
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samtools view -T $fasta $input $fai_reference -@ $task.cpus -o $input_out
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samtools index -b $input_out -@ $task.cpus
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bamCoverage \\
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--bam $input_out \\
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$args \\
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--numberOfProcessors ${task.cpus} \\
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--outFileName ${prefix}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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deeptools: \$(bamCoverage --version | sed -e "s/bamCoverage //g")
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END_VERSIONS
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"""
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}
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else {
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"""
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bamCoverage \\
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--bam $input_out \\
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$args \\
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--numberOfProcessors ${task.cpus} \\
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--outFileName ${prefix}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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deeptools: \$(bamCoverage --version | sed -e "s/bamCoverage //g")
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END_VERSIONS
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"""
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}
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}
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