Add AdapterRemovalFixPrefix (#1424)

* Add AdapterRemovalFixPrefix

* Prettifying

Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com>
This commit is contained in:
James A. Fellows Yates 2022-03-21 11:26:12 +01:00 committed by GitHub
parent 5297d27fbf
commit 8c00897853
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6 changed files with 122 additions and 0 deletions

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@ -0,0 +1,38 @@
def VERSION = '0.05'
process ADAPTERREMOVALFIXPREFIX {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::adapterremovalfixprefix=0.0.5" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/adapterremovalfixprefix:0.0.5--hdfd78af_2':
'quay.io/biocontainers/adapterremovalfixprefix:0.0.5--hdfd78af_2' }"
input:
tuple val(meta), path(fastq)
output:
tuple val(meta), path("*.fq.gz"), emit: fixed_fastq
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
if ("$fastq" == "${prefix}.fq.gz") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
"""
AdapterRemovalFixPrefix \\
$fastq \\
$args \\
| gzip > ${prefix}.fq.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
adapterremovalfixprefix: $VERSION
END_VERSIONS
"""
}

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@ -0,0 +1,43 @@
name: adapterremovalfixprefix
description: Fixes prefixes from AdapterRemoval2 output to make sure no clashing read names are in the output. For use with DeDup.
keywords:
- adapterremoval
- fastq
- dedup
tools:
- adapterremovalfixprefix:
description: Fixes adapter removal prefixes to make sure no clashing read names are in the output.
homepage: https://github.com/apeltzer/AdapterRemovalFixPrefix
documentation: None
tool_dev_url: https://github.com/apeltzer/AdapterRemovalFixPrefix
doi: "10.1186/s13059-016-0918-z"
licence: ["GPL v3"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- fastq:
type: file
description: FASTQ file from AdapterRemoval2
pattern: "*.{fq.gz,fastq.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"
- fixed_fastq:
type: file
description: FASTQ file with fixed read prefixes for DeDup
pattern: "*.{fq.gz}"
authors:
- "@jfy133"

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@ -14,6 +14,10 @@ adapterremoval:
- modules/adapterremoval/**
- tests/modules/adapterremoval/**
adapterremovalfixprefix:
- modules/adapterremovalfixprefix/**
- tests/modules/adapterremovalfixprefix/**
agrvate:
- modules/agrvate/**
- tests/modules/agrvate/**

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@ -0,0 +1,19 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { ADAPTERREMOVAL } from '../../../modules/adapterremoval/main.nf'
include { ADAPTERREMOVALFIXPREFIX } from '../../../modules/adapterremovalfixprefix/main.nf'
workflow test_adapterremovalfixprefix {
input = [
[ id:'test', single_end:false ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
]
]
ADAPTERREMOVAL ( input, [] )
ADAPTERREMOVALFIXPREFIX ( ADAPTERREMOVAL.out.collapsed )
}

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@ -0,0 +1,9 @@
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: ADAPTERREMOVAL {
ext.args = "--collapse"
}
}

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@ -0,0 +1,9 @@
- name: adapterremovalfixprefix test_adapterremovalfixprefix
command: nextflow run tests/modules/adapterremovalfixprefix -entry test_adapterremovalfixprefix -c tests/config/nextflow.config
tags:
- adapterremovalfixprefix
files:
- path: output/adapterremovalfixprefix/test.fq.gz
md5sum: ff956de3532599a56c3efe5369f0953f
- path: output/adapterremovalfixprefix/versions.yml
md5sum: 983cb58079bf015c1d489a7e48261746