nf-core_modules/tests/modules/genrich/main.nf
Jose Espinosa-Carrasco 0a7368aa6f
Refactor genrich to avoid params in main (#981)
* Refactor genrich to avoid params in main

* Missed to commit test.yml file
2021-10-29 16:37:39 +02:00

79 lines
3.1 KiB
Text

#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { GENRICH } from '../../../modules/genrich/main.nf' addParams( options: ["args": "-p 0.1"] )
include { GENRICH as GENRICH_CTRL } from '../../../modules/genrich/main.nf' addParams( options: ["args": "-p 0.9"] )
include { GENRICH as GENRICH_ALL } from '../../../modules/genrich/main.nf' addParams( options: ["args": "-r -p 0.1"] )
include { GENRICH as GENRICH_ATACSEQ } from '../../../modules/genrich/main.nf' addParams( options: ["args": "-j -p 0.1"] )
workflow test_genrich {
input = [ [ id:'test', single_end:false ], // meta map
[ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ]]
control = [ ]
blacklist = [ ]
save_pvalues = false
save_pileup = false
save_bed = false
save_duplicates = false
GENRICH ( input, control, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
}
workflow test_genrich_ctrl {
input = [ [ id:'test', single_end:false ], // meta map
[ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ]]
control = [ file( params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true) ]
blacklist = [ ]
save_pvalues = false
save_pileup = false
save_bed = false
save_duplicates = false
GENRICH_CTRL ( input, control, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
}
workflow test_genrich_all_outputs {
input = [ [ id:'test', single_end:false ], // meta map
[ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ]]
control = [ file( params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true) ]
blacklist = [ ]
save_pvalues = true
save_pileup = true
save_bed = true
save_duplicates = true
GENRICH_ALL ( input, control, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
}
workflow test_genrich_blacklist {
input = [ [ id:'test', single_end:false ], // meta map
[ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ]]
control = [ ]
blacklist = [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)]
save_pvalues = false
save_pileup = false
save_bed = false
save_duplicates = false
GENRICH ( input, control, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
}
workflow test_genrich_atacseq {
input = [ [ id:'test', single_end:false ], // meta map
[ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ]]
control = [ ]
blacklist = [ ]
save_pvalues = false
save_pileup = false
save_bed = false
save_duplicates = false
GENRICH_ATACSEQ ( input, control, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
}