mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-26 23:43:19 -05:00
45 lines
1.5 KiB
Text
45 lines
1.5 KiB
Text
|
#!/usr/bin/env nextflow
|
||
|
|
|
||
|
|
nextflow.enable.dsl = 2
|
||
|
|
|
||
|
|
include { SAMTOOLS_AMPLICONCLIP } from '../../../../modules/samtools/ampliconclip/main.nf' addParams([:])
|
||
|
|
|
||
|
|
workflow test_samtools_ampliconclip_no_stats_no_rejects {
|
||
|
|
|
||
|
|
input = [
|
||
|
|
[ id:'test', single_end:false ],
|
||
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
|
||
|
|
]
|
||
|
|
bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
|
||
|
|
save_cliprejects = false
|
||
|
|
save_clipstats = false
|
||
|
|
|
||
|
|
SAMTOOLS_AMPLICONCLIP ( input, bed, save_cliprejects, save_clipstats )
|
||
|
|
}
|
||
|
|
|
||
|
|
workflow test_samtools_ampliconclip_no_stats_with_rejects {
|
||
|
|
|
||
|
|
input = [
|
||
|
|
[ id:'test', single_end:false ],
|
||
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
|
||
|
|
]
|
||
|
|
bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
|
||
|
|
save_cliprejects = true
|
||
|
|
save_clipstats = false
|
||
|
|
|
||
|
|
SAMTOOLS_AMPLICONCLIP ( input, bed, save_cliprejects, save_clipstats )
|
||
|
|
}
|
||
|
|
|
||
|
|
workflow test_samtools_ampliconclip_with_stats_with_rejects {
|
||
|
|
|
||
|
|
input = [
|
||
|
|
[ id:'test', single_end:false ],
|
||
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
|
||
|
|
]
|
||
|
|
bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
|
||
|
|
save_cliprejects = true
|
||
|
|
save_clipstats = true
|
||
|
|
|
||
|
|
SAMTOOLS_AMPLICONCLIP ( input, bed, save_cliprejects, save_clipstats )
|
||
|
|
}
|