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