mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 21:53:10 +00:00
e971f538a9
* Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Fix IQ tree * Fix picard markdup and merge sam * Fix plink/vcf version * Fix plink version output * Fix prokka version command * Fix pydamage * Try fixing markduplicates * Fix snpEff * Fix vcftools version * Fix pydamage and filtersamreads test run * Fix MarkDuplicates tests * Add missing unsorted checks * Remove MD5 sym due to stochasicity in BAM file
22 lines
913 B
Text
22 lines
913 B
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { PICARD_MARKDUPLICATES } from '../../../../modules/picard/markduplicates/main.nf' addParams( options: [:] )
|
|
include { PICARD_MARKDUPLICATES as PICARD_MARKDUPLICATES_UNSORTED} from '../../../../modules/picard/markduplicates/main.nf' addParams( options: [args : '--ASSUME_SORT_ORDER queryname' ] )
|
|
|
|
workflow test_picard_markduplicates_sorted_bam {
|
|
input = [ [ id:'test', single_end:false ], // meta map
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
|
|
]
|
|
|
|
PICARD_MARKDUPLICATES ( input )
|
|
}
|
|
|
|
workflow test_picard_markduplicates_unsorted_bam {
|
|
input = [ [ id:'test', single_end:false ], // meta map
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
|
|
]
|
|
|
|
PICARD_MARKDUPLICATES_UNSORTED ( input )
|
|
}
|