mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
f62e4cf5f0
* Added Somalier extract module * changed somalier_dbg4 to somalier for versions.yml * added and minor changes in meta.yml * Apply suggestions from code review * Update main.nf * Typo in quay.io rl * updated the input * new updates * linting * linting * changed the test.yml * Update modules/somalier/extract/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/somalier/extract/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/somalier/extract/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/somalier/extract/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update tests/modules/somalier/extract/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/somalier/extract/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update tests/modules/somalier/extract/test.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * last changes * Update modules/somalier/extract/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/somalier/extract/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/somalier/extract/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
23 lines
913 B
Text
23 lines
913 B
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { SOMALIER_EXTRACT } from '../../../../modules/somalier/extract/main.nf'
|
|
|
|
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
|
|
|
|
fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
|
|
|
|
sites = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/somalier/sites_chr21.hg38.vcf.gz", checkIfExists: true)
|
|
|
|
|
|
workflow test_somalier_extract {
|
|
|
|
input = [
|
|
[ id:'test', single_end:false ], // meta map
|
|
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam'], checkIfExists: true),
|
|
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam_bai'], checkIfExists: true)
|
|
]
|
|
|
|
SOMALIER_EXTRACT ( input, [fasta, fasta_fai], sites )
|
|
}
|