mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-10 21:53:09 +00:00
Add Porechop module
This commit is contained in:
parent
b23fb927a9
commit
16be676d72
4 changed files with 97 additions and 0 deletions
|
@ -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}_${meta.run_accession}_processed" }
|
||||
|
|
|
@ -23,6 +23,9 @@
|
|||
},
|
||||
"multiqc": {
|
||||
"git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
|
||||
},
|
||||
"porechop": {
|
||||
"git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
35
modules/nf-core/modules/porechop/main.nf
generated
Normal file
35
modules/nf-core/modules/porechop/main.nf
generated
Normal file
|
@ -0,0 +1,35 @@
|
|||
process PORECHOP {
|
||||
tag "$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
|
||||
"""
|
||||
}
|
50
modules/nf-core/modules/porechop/meta.yml
generated
Normal file
50
modules/nf-core/modules/porechop/meta.yml
generated
Normal file
|
@ -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"
|
Loading…
Reference in a new issue