diff --git a/tests/modules/mosdepth/main.nf b/tests/modules/mosdepth/main.nf index dd4a01c4..1bb8e8ff 100644 --- a/tests/modules/mosdepth/main.nf +++ b/tests/modules/mosdepth/main.nf @@ -8,90 +8,89 @@ include { MOSDEPTH as MOSDEPTH_WINDOW } from '../../../modules/mosdepth/main. include { MOSDEPTH as MOSDEPTH_THRESHOLD } from '../../../modules/mosdepth/main.nf' include { MOSDEPTH as MOSDEPTH_QUANTIZED } from '../../../modules/mosdepth/main.nf' - workflow test_mosdepth { - input = [ - [ id:'test', single_end:true ], - [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ], - [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ] - ] + input = [ + [ id:'test', single_end:true ], + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) + ] MOSDEPTH ( input, [], [] ) } workflow test_mosdepth_bed { - input = [ - [ id:'test', single_end:true ], - [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ], - [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ] - ] - bed = [ file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) ] + input = [ + [ id:'test', single_end:true ], + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) + ] + bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) MOSDEPTH ( input, bed, [] ) } workflow test_mosdepth_cram { - input = [ - [ id:'test', single_end:true ], - [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true) ], - [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true) ] - ] - fasta = [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ] + input = [ + [ id:'test', single_end:true ], + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true) + ] + fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) MOSDEPTH ( input, [], fasta ) } workflow test_mosdepth_cram_bed { input = [ - [ id:'test', single_end:true ], - [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true) ], - [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true) ] - ] - bed = [ file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) ] - fasta = [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ] + [ id:'test', single_end:true ], + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true) + ] + bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) MOSDEPTH ( input, bed, fasta ) } workflow test_mosdepth_window { - input = [ - [ id:'test', single_end:true ], - [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ], - [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ] - ] - bed = [ file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) ] + input = [ + [ id:'test', single_end:true ], + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) + ] + bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) MOSDEPTH_WINDOW ( input, [], [] ) } workflow test_mosdepth_quantized { - input = [ - [ id:'test', single_end:true ], - [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ], - [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ] - ] + input = [ + [ id:'test', single_end:true ], + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) + ] MOSDEPTH_QUANTIZED ( input, [], [] ) } workflow test_mosdepth_thresholds { - input = [ - [ id:'test', single_end:true ], - [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ], - [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ] - ] - bed = [ file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) ] + input = [ + [ id:'test', single_end:true ], + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) + ] + bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) MOSDEPTH_THRESHOLD ( input, bed, [] ) } workflow test_mosdepth_fail { - input = [ - [ id:'test', single_end:true ], - [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ], - [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ] - ] - bed = [ file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) ] + input = [ + [ id:'test', single_end:true ], + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) + ] + bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) MOSDEPTH_FAIL ( input, bed, [] ) }