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https://github.com/MillironX/nf-core_modules.git
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a6e0629e24
* Change intervals to be part of sample specific input * Fix some tests * Update checksum * Update intervals * Update intervals * Try out gavins idea for adding the file * update test line * update test line * update test line * revert contains line
47 lines
2.6 KiB
Text
47 lines
2.6 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GATK4_APPLYBQSR } from '../../../../modules/gatk4/applybqsr/main.nf'
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workflow test_gatk4_applybqsr {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_baserecalibrator_table'], checkIfExists: true),
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[]
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
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dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
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GATK4_APPLYBQSR ( input, fasta, fai, dict )
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}
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workflow test_gatk4_applybqsr_intervals {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_baserecalibrator_table'], checkIfExists: true),
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file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
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dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
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GATK4_APPLYBQSR ( input, fasta, fai, dict )
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}
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workflow test_gatk4_applybqsr_cram {
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input = [ [ id:'test' ], // 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']['illumina']['test_baserecalibrator_table'], 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_APPLYBQSR ( input, fasta, fai, dict )
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}
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