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eab173f2bb
* Added java options to vardict java * updated test.yml * correctly added java options * Added automatic version numbers for vardictjava * possible fix for version number in conda * removed the cram tests * linting * Update modules/vardictjava/main.nf Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> * Update modules/vardictjava/main.nf Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> * removed the version line Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
20 lines
813 B
Text
20 lines
813 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { VARDICTJAVA } from '../../../modules/vardictjava/main.nf'
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workflow test_vardictjava_bam {
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bam_input_ch = Channel.value([
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[ id:'test' ], // 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 = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
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VARDICTJAVA ( bam_input_ch, fasta, fasta_fai )
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}
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