millironx/nf-core_modules
1
0
Fork 0
mirror of https://github.com/MillironX/nf-core_modules.git synced 2024-09-20 23:32:05 +00:00
Code Issues Releases Packages Activity

Update main.nf

Browse source
This commit is contained in:
Harshil Patel 2022-05-25 19:38:12 +01:00 committed by GitHub
parent bc7002b0c9
commit 241a1de035
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
1 changed files with 46 additions and 47 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

93
tests/modules/mosdepth/main.nf
View file

@ -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, [] )
}