mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
682f789f93
* Bump tool versions for modules required in viralrecon * Fix all the tests * Fix Prettier lint * Remove empty md5sums
55 lines
1.3 KiB
Text
55 lines
1.3 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { FASTQC } from '../../../../modules/fastqc/main.nf'
|
|
include { MULTIQC } from '../../../../modules/multiqc/main.nf'
|
|
include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../../../modules/custom/dumpsoftwareversions/main.nf'
|
|
|
|
workflow fastqc1 {
|
|
take:
|
|
input
|
|
|
|
main:
|
|
FASTQC ( input )
|
|
|
|
emit:
|
|
versions = FASTQC.out.versions
|
|
}
|
|
|
|
workflow fastqc2 {
|
|
take:
|
|
input
|
|
|
|
main:
|
|
FASTQC ( input )
|
|
|
|
emit:
|
|
versions = FASTQC.out.versions
|
|
zip = FASTQC.out.zip
|
|
}
|
|
|
|
workflow test_custom_dumpsoftwareversions {
|
|
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_2_fastq_gz'], checkIfExists: true)
|
|
]
|
|
]
|
|
|
|
// Using subworkflows to ensure that the script can properly handle
|
|
// cases where subworkflows have a module with the same name.
|
|
fastqc1 ( input )
|
|
fastqc2 ( input )
|
|
MULTIQC ( fastqc2.out.zip.collect { it[1] }, [[],[]] )
|
|
|
|
fastqc1
|
|
.out
|
|
.versions
|
|
.mix(fastqc2.out.versions)
|
|
.mix(MULTIQC.out.versions)
|
|
.set { ch_software_versions }
|
|
|
|
CUSTOM_DUMPSOFTWAREVERSIONS ( ch_software_versions.collectFile() )
|
|
}
|