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Merge pull request #165 from genomic-medicine-sweden/fix_porechop_conflict

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Fix porechop conflict
This commit is contained in:
James A. Fellows Yates 2022-11-03 14:08:13 +01:00 committed by GitHub
commit bc671c547d
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5 changed files with 14 additions and 15 deletions
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2
conf/modules.config
View file

@ -132,7 +132,7 @@ process {
] ]
} }
withName: PORECHOP { withName: PORECHOP_PORECHOP {
ext.prefix = { "${meta.id}_${meta.run_accession}" } ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [ publishDir = [
path: { "${params.outdir}/porechop" }, path: { "${params.outdir}/porechop" },

4
modules.json
View file

@ -141,9 +141,9 @@
"branch": "master", "branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
}, },
"porechop": { "porechop/porechop": {
"branch": "master", "branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" "git_sha": "2a4e85eb81875a572bb58133e37f84ba3cc484d7"
}, },
"prinseqplusplus": { "prinseqplusplus": {
"branch": "master", "branch": "master",

3
modules/nf-core/porechop/main.nf → modules/nf-core/porechop/porechop/main.nf generated
View file

@ -1,4 +1,4 @@
process PORECHOP { process PORECHOP_PORECHOP {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
@ -28,7 +28,6 @@ process PORECHOP {
$args \\ $args \\
-o ${prefix}.fastq.gz \\ -o ${prefix}.fastq.gz \\
> ${prefix}.log > ${prefix}.log
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
porechop: \$( porechop --version ) porechop: \$( porechop --version )

2
modules/nf-core/porechop/meta.yml → modules/nf-core/porechop/porechop/meta.yml generated
View file

@ -1,4 +1,4 @@
name: porechop name: "porechop_porechop"
description: Adapter removal and demultiplexing of Oxford Nanopore reads description: Adapter removal and demultiplexing of Oxford Nanopore reads
keywords: keywords:
- adapter - adapter

18
subworkflows/local/longread_preprocessing.nf
View file

@ -5,7 +5,7 @@
include { FASTQC as FASTQC_PROCESSED } from '../../modules/nf-core/fastqc/main' include { FASTQC as FASTQC_PROCESSED } from '../../modules/nf-core/fastqc/main'
include { FALCO as FALCO_PROCESSED } from '../../modules/nf-core/falco/main' include { FALCO as FALCO_PROCESSED } from '../../modules/nf-core/falco/main'
include { PORECHOP } from '../../modules/nf-core/porechop/main' include { PORECHOP_PORECHOP } from '../../modules/nf-core/porechop/porechop/main'
include { FILTLONG } from '../../modules/nf-core/filtlong/main' include { FILTLONG } from '../../modules/nf-core/filtlong/main'
workflow LONGREAD_PREPROCESSING { workflow LONGREAD_PREPROCESSING {
@ -17,9 +17,9 @@ workflow LONGREAD_PREPROCESSING {
ch_multiqc_files = Channel.empty() ch_multiqc_files = Channel.empty()
if ( !params.longread_qc_skipadaptertrim && params.longread_qc_skipqualityfilter) { if ( !params.longread_qc_skipadaptertrim && params.longread_qc_skipqualityfilter) {
PORECHOP ( reads ) PORECHOP_PORECHOP ( reads )
ch_processed_reads = PORECHOP.out.reads ch_processed_reads = PORECHOP_PORECHOP.out.reads
.map { .map {
meta, reads -> meta, reads ->
def meta_new = meta.clone() def meta_new = meta.clone()
@ -27,8 +27,8 @@ workflow LONGREAD_PREPROCESSING {
[ meta_new, reads ] [ meta_new, reads ]
} }
ch_versions = ch_versions.mix(PORECHOP.out.versions.first()) ch_versions = ch_versions.mix(PORECHOP_PORECHOP.out.versions.first())
ch_multiqc_files = ch_multiqc_files.mix( PORECHOP.out.log ) ch_multiqc_files = ch_multiqc_files.mix( PORECHOP_PORECHOP.out.log )
} else if ( params.longread_qc_skipadaptertrim && !params.longread_qc_skipqualityfilter) { } else if ( params.longread_qc_skipadaptertrim && !params.longread_qc_skipqualityfilter) {
@ -37,8 +37,8 @@ workflow LONGREAD_PREPROCESSING {
ch_multiqc_files = ch_multiqc_files.mix( FILTLONG.out.log ) ch_multiqc_files = ch_multiqc_files.mix( FILTLONG.out.log )
} else { } else {
PORECHOP ( reads ) PORECHOP_PORECHOP ( reads )
ch_clipped_reads = PORECHOP.out.reads ch_clipped_reads = PORECHOP_PORECHOP.out.reads
.map { .map {
meta, reads -> meta, reads ->
def meta_new = meta.clone() def meta_new = meta.clone()
@ -48,9 +48,9 @@ workflow LONGREAD_PREPROCESSING {
ch_processed_reads = FILTLONG ( ch_clipped_reads.map{ meta, reads -> [meta, [], reads ]} ).reads ch_processed_reads = FILTLONG ( ch_clipped_reads.map{ meta, reads -> [meta, [], reads ]} ).reads
ch_versions = ch_versions.mix(PORECHOP.out.versions.first()) ch_versions = ch_versions.mix(PORECHOP_PORECHOP.out.versions.first())
ch_versions = ch_versions.mix(FILTLONG.out.versions.first()) ch_versions = ch_versions.mix(FILTLONG.out.versions.first())
ch_multiqc_files = ch_multiqc_files.mix( PORECHOP.out.log ) ch_multiqc_files = ch_multiqc_files.mix( PORECHOP_PORECHOP.out.log )
ch_multiqc_files = ch_multiqc_files.mix( FILTLONG.out.log ) ch_multiqc_files = ch_multiqc_files.mix( FILTLONG.out.log )
} }