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57b43ed3de
* Update meta.yml by fixing html pattern expected Fixed html pattern typo: Before: pattern: "*.thml" After fix: pattern: "*.html" * main.nf for bbmap_clumpify * meta.yml for bbmap_clumpify * bbmap/clumpify via Gitpod and @mahesh-panchal guide * small changes to tests * explicit mention of output file pattern - *.clumped.fastq.gz * Update modules/bbmap/clumpify/main.nf Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> * Update modules/bbmap/clumpify/main.nf Accepted @mahesh-panchal suggestions Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
38 lines
1.2 KiB
Text
38 lines
1.2 KiB
Text
process BBMAP_CLUMPIFY {
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tag "$meta.id"
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label 'process_single'
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label 'process_high_memory'
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conda (params.enable_conda ? "bioconda::bbmap=38.98" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bbmap:38.98--h5c4e2a8_1' :
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'quay.io/biocontainers/bbmap:38.98--h5c4e2a8_1' }"
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input:
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tuple val(meta), path(reads)
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output:
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tuple val(meta), path('*.fastq.gz'), emit: reads
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tuple val(meta), path('*.log') , emit: log
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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 ?: "${meta.id}"
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def raw = meta.single_end ? "in=$reads" : "in1=${reads[0]} in2=${reads[1]}"
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def clumped = meta.single_end ? "out=${prefix}.clumped.fastq.gz" : "out1=${prefix}_1.clumped.fastq.gz out2=${prefix}_2.clumped.fastq.gz"
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"""
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clumpify.sh \\
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$raw \\
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$clumped \\
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$args \\
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&> ${prefix}.clumpify.log
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bbmap: \$(bbversion.sh)
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END_VERSIONS
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"""
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}
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