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Add Porechop module

This commit is contained in:
ljmesi 2022-03-18 14:34:10 +01:00
parent b23fb927a9
commit 16be676d72
4 changed files with 97 additions and 0 deletions

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@ -50,6 +50,15 @@ process {
]
}
withName: PORECHOP {
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
path: { "${params.outdir}/porechop" },
mode: 'copy',
pattern: '*.fastq.gz'
]
}
withName: FASTQC_POST {
ext.args = '--quiet'
ext.prefix = { "${meta.id}_${meta.run_accession}_processed" }

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@ -23,6 +23,9 @@
},
"multiqc": {
"git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
},
"porechop": {
"git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
}
}
}

35
modules/nf-core/modules/porechop/main.nf generated Normal file
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@ -0,0 +1,35 @@
process PORECHOP {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::porechop=0.2.4" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/porechop:0.2.4--py39h7cff6ad_2' :
'quay.io/biocontainers/porechop:0.2.4--py39h7cff6ad_2' }"
input:
tuple val(meta), path(reads)
output:
tuple val(meta), path("*.fastq.gz"), emit: reads
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
porechop \\
-i $reads \\
-t $task.cpus \\
$args \\
-o ${prefix}.fastq.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
porechop: \$( porechop --version )
END_VERSIONS
"""
}

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@ -0,0 +1,50 @@
name: porechop
description: Adapter removal and demultiplexing of Oxford Nanopore reads
keywords:
- adapter
- nanopore
- demultiplexing
tools:
- porechop:
description: Adapter removal and demultiplexing of Oxford Nanopore reads
homepage: "https://github.com/rrwick/Porechop"
documentation: "https://github.com/rrwick/Porechop"
tool_dev_url: "https://github.com/rrwick/Porechop"
doi: "10.1099/mgen.0.000132"
licence: ["GPL v3"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: fastq/fastq.gz file
pattern: "*.{fastq,fastq.gz,fq,fq.gz}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- reads:
type: file
description: Demultiplexed and/or adapter-trimmed fastq.gz file
pattern: "*.{fastq.gz}"
authors:
- "@ggabernet"
- "@jasmezz"
- "@d4straub"
- "@LaurenceKuhl"
- "@SusiJo"
- "@jonasscheid"
- "@jonoave"
- "@GokceOGUZ"