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possible fix for name collisions

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This commit is contained in:
Matthias De Smet 2022-06-07 13:58:27 +02:00
parent 59ce1ec348
commit e5bf87aec3
4 changed files with 32 additions and 8 deletions
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2
modules/multiqc/main.nf
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@ -7,7 +7,7 @@ process MULTIQC {
'quay.io/biocontainers/multiqc:1.12--pyhdfd78af_0' }" 'quay.io/biocontainers/multiqc:1.12--pyhdfd78af_0' }"
input: input:
path multiqc_files path "??/*"
output: output:
path "*multiqc_report.html", emit: report path "*multiqc_report.html", emit: report

23
tests/modules/multiqc/main.nf
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@ -2,15 +2,30 @@
nextflow.enable.dsl = 2 nextflow.enable.dsl = 2
include { FASTQC } from '../../../modules/fastqc/main.nf' include { FASTQC } from '../../../modules/fastqc/main.nf'
include { MULTIQC } from '../../../modules/multiqc/main.nf' include { FASTQC as FASTQC2 } from '../../../modules/fastqc/main.nf'
include { MULTIQC } from '../../../modules/multiqc/main.nf'
workflow test_multiqc { workflow test_multiqc {
input = [ [ id: 'test', single_end: false ], input = [ [ id: 'test', single_end: false ],
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
] ]
FASTQC ( input ) FASTQC ( input )
MULTIQC ( FASTQC.out.zip.collect { it[1] } ) MULTIQC ( FASTQC.out.zip.collect { it[1] } )
} }
workflow test_multiqc_fn_collision {
fqc_input = [ [ id: 'test', single_end: false ],
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
]
mqc_input = Channel.empty()
FASTQC ( fqc_input )
mqc_input = mqc_input.mix(FASTQC.out.zip.collect { it[1] })
FASTQC2 ( fqc_input )
mqc_input = mqc_input.mix(FASTQC2.out.zip.collect { it[1] })
MULTIQC ( mqc_input )
}

4
tests/modules/multiqc/nextflow.config
View file

@ -1,5 +1,7 @@
process { process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: "FASTQC*" {
publishDir = [ enabled: false ]
}
} }

11
tests/modules/multiqc/test.yml
View file

@ -1,5 +1,12 @@
- name: multiqc - name: multiqc test_multiqc
command: nextflow run ./tests/modules/multiqc -entry test_multiqc -c ./tests/config/nextflow.config -c ./tests/modules/multiqc/nextflow.config command: nextflow run ./tests/modules/multiqc -entry test_multiqc -c ./tests/config/nextflow.config -c ./tests/modules/multiqc/nextflow.config
tags:
- multiqc
files:
- path: output/multiqc/multiqc_report.html
- name: multiqc test_multiqc_fn_collision
command: nextflow run ./tests/modules/multiqc -entry test_multiqc_fn_collision -c ./tests/config/nextflow.config -c ./tests/modules/multiqc/nextflow.config
tags: tags:
- multiqc - multiqc
files: files: