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Update main.nf

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Harshil Patel 2022-05-25 19:38:12 +01:00 committed by GitHub
parent bc7002b0c9
commit 241a1de035
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1 changed files with 46 additions and 47 deletions
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tests/modules/mosdepth/main.nf
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@ -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_THRESHOLD } from '../../../modules/mosdepth/main.nf'
include { MOSDEPTH as MOSDEPTH_QUANTIZED } from '../../../modules/mosdepth/main.nf' include { MOSDEPTH as MOSDEPTH_QUANTIZED } from '../../../modules/mosdepth/main.nf'
workflow test_mosdepth { workflow test_mosdepth {
input = [ input = [
[ id:'test', single_end:true ], [ 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'], checkIfExists: true),
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ] file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
] ]
MOSDEPTH ( input, [], [] ) MOSDEPTH ( input, [], [] )
} }
workflow test_mosdepth_bed { workflow test_mosdepth_bed {
input = [ input = [
[ id:'test', single_end:true ], [ 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'], checkIfExists: true),
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], 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) ] bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
MOSDEPTH ( input, bed, [] ) MOSDEPTH ( input, bed, [] )
} }
workflow test_mosdepth_cram { workflow test_mosdepth_cram {
input = [ input = [
[ id:'test', single_end: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'], checkIfExists: true),
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], 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) ] fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
MOSDEPTH ( input, [], fasta ) MOSDEPTH ( input, [], fasta )
} }
workflow test_mosdepth_cram_bed { workflow test_mosdepth_cram_bed {
input = [ input = [
[ id:'test', single_end: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'], checkIfExists: true),
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], 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) ] bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
fasta = [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ] fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
MOSDEPTH ( input, bed, fasta ) MOSDEPTH ( input, bed, fasta )
} }
workflow test_mosdepth_window { workflow test_mosdepth_window {
input = [ input = [
[ id:'test', single_end:true ], [ 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'], checkIfExists: true),
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], 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) ] bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
MOSDEPTH_WINDOW ( input, [], [] ) MOSDEPTH_WINDOW ( input, [], [] )
} }
workflow test_mosdepth_quantized { workflow test_mosdepth_quantized {
input = [ input = [
[ id:'test', single_end:true ], [ 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'], checkIfExists: true),
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ] file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
] ]
MOSDEPTH_QUANTIZED ( input, [], [] ) MOSDEPTH_QUANTIZED ( input, [], [] )
} }
workflow test_mosdepth_thresholds { workflow test_mosdepth_thresholds {
input = [ input = [
[ id:'test', single_end:true ], [ 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'], checkIfExists: true),
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], 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) ] bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
MOSDEPTH_THRESHOLD ( input, bed, [] ) MOSDEPTH_THRESHOLD ( input, bed, [] )
} }
workflow test_mosdepth_fail { workflow test_mosdepth_fail {
input = [ input = [
[ id:'test', single_end:true ], [ 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'], checkIfExists: true),
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], 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) ] bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
MOSDEPTH_FAIL ( input, bed, [] ) MOSDEPTH_FAIL ( input, bed, [] )
} }