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5a30294eec
* updated the delly/call module * Update modules/delly/call/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
44 lines
2.1 KiB
Text
44 lines
2.1 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { DELLY_CALL } from '../../../../modules/delly/call/main.nf'
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workflow test_delly_call_bam {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
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]
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exclude_regions = []
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
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fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
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DELLY_CALL ( input, exclude_regions, fasta, fai )
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}
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workflow test_delly_call_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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]
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exclude_regions = []
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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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DELLY_CALL ( input, exclude_regions, fasta, fai )
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}
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workflow test_delly_call_exclude_regions {
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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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]
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exclude_regions = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
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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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DELLY_CALL ( input, exclude_regions, fasta, fai )
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}
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