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45 lines
2.5 KiB
Text
45 lines
2.5 KiB
Text
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GENRICH } from '../../../modules/genrich/main.nf' addParams( control_bam: false, pvalues: false, pileup:false, bed:false, blacklist_bed:false, save_duplicates:false, options: ["args": "-p 0.1"] )
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include { GENRICH as GENRICH_BLACKLIST } from '../../../modules/genrich/main.nf' addParams( control_bam: false, pvalues: false, pileup:false, bed:false, blacklist_bed:true, save_duplicates:false, options: ["args": "-p 0.1"] )
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include { GENRICH as GENRICH_ALL_OUTPUTS } from '../../../modules/genrich/main.nf' addParams( control_bam: false, pvalues: true, pileup:true, bed:true, blacklist_bed:false, save_duplicates:true, options: ["args": "-r -p 0.1"] )
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include { GENRICH as GENRICH_ATACSEQ } from '../../../modules/genrich/main.nf' addParams( control_bam: false, pvalues: false, pileup:false, bed:false, blacklist_bed:false, save_duplicates:false, 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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GENRICH ( input, control, blacklist )
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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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GENRICH ( input, control, blacklist )
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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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GENRICH_ALL_OUTPUTS ( input, control, blacklist )
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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 = [ file( params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true) ]
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blacklist = [ ]
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GENRICH_ATACSEQ ( input, control, blacklist )
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}
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