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09acfad211
* added the module * updated test.yml * Update modules/gatk4/collectreadcounts/main.nf Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * small fix * tests update * linting * tests update (again) Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
54 lines
2 KiB
Text
54 lines
2 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GATK4_COLLECTREADCOUNTS } from '../../../../modules/gatk4/collectreadcounts/main.nf'
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workflow test_gatk4_collectreadcounts_hdf5 {
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input = [
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[ id:'test', single_end:false ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true),
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]
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fasta = []
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fai = []
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dict = []
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GATK4_COLLECTREADCOUNTS ( input, fasta, fai, dict )
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}
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workflow test_gatk4_collectreadcounts_tsv {
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input = [
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[ id:'test', single_end:false ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true),
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]
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fasta = []
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fai = []
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dict = []
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GATK4_COLLECTREADCOUNTS ( input, fasta, fai, dict )
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}
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workflow test_gatk4_collectreadcounts_cram {
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input = [
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[ id:'test', single_end:false ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true),
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
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dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
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GATK4_COLLECTREADCOUNTS ( input, fasta, fai, dict )
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}
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