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Add Porechop module
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parent
b23fb927a9
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4 changed files with 97 additions and 0 deletions
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@ -50,6 +50,15 @@ process {
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]
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]
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}
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}
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withName: PORECHOP {
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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path: { "${params.outdir}/porechop" },
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mode: 'copy',
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pattern: '*.fastq.gz'
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]
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}
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withName: FASTQC_POST {
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withName: FASTQC_POST {
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ext.args = '--quiet'
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ext.args = '--quiet'
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ext.prefix = { "${meta.id}_${meta.run_accession}_processed" }
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ext.prefix = { "${meta.id}_${meta.run_accession}_processed" }
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@ -23,6 +23,9 @@
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},
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},
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"multiqc": {
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"multiqc": {
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"git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
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"git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
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},
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"porechop": {
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"git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
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}
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}
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}
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}
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}
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}
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35
modules/nf-core/modules/porechop/main.nf
generated
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35
modules/nf-core/modules/porechop/main.nf
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@ -0,0 +1,35 @@
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process PORECHOP {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::porechop=0.2.4" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/porechop:0.2.4--py39h7cff6ad_2' :
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'quay.io/biocontainers/porechop:0.2.4--py39h7cff6ad_2' }"
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input:
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tuple val(meta), path(reads)
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output:
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tuple val(meta), path("*.fastq.gz"), emit: reads
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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porechop \\
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-i $reads \\
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-t $task.cpus \\
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$args \\
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-o ${prefix}.fastq.gz
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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porechop: \$( porechop --version )
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END_VERSIONS
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"""
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}
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50
modules/nf-core/modules/porechop/meta.yml
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50
modules/nf-core/modules/porechop/meta.yml
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name: porechop
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description: Adapter removal and demultiplexing of Oxford Nanopore reads
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keywords:
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- adapter
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- nanopore
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- demultiplexing
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tools:
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- porechop:
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description: Adapter removal and demultiplexing of Oxford Nanopore reads
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homepage: "https://github.com/rrwick/Porechop"
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documentation: "https://github.com/rrwick/Porechop"
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tool_dev_url: "https://github.com/rrwick/Porechop"
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doi: "10.1099/mgen.0.000132"
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licence: ["GPL v3"]
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- reads:
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type: file
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description: fastq/fastq.gz file
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pattern: "*.{fastq,fastq.gz,fq,fq.gz}"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- reads:
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type: file
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description: Demultiplexed and/or adapter-trimmed fastq.gz file
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pattern: "*.{fastq.gz}"
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authors:
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- "@ggabernet"
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- "@jasmezz"
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- "@d4straub"
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- "@LaurenceKuhl"
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- "@SusiJo"
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- "@jonasscheid"
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- "@jonoave"
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- "@GokceOGUZ"
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