mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 02:58:17 +00:00
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
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { VARDICTJAVA } from '../../../modules/vardictjava/main.nf'
|
|
|
|
workflow test_vardictjava_bam {
|
|
|
|
bam_input_ch = Channel.value([
|
|
[ id:'test' ], // meta map
|
|
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
|
|
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
|
|
file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
|
|
])
|
|
|
|
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
|
fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
|
|
|
VARDICTJAVA ( bam_input_ch, fasta, fasta_fai )
|
|
}
|