mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-15 22:23:09 +00:00
28 lines
744 B
Text
28 lines
744 B
Text
|
#!/usr/bin/env nextflow
|
||
|
|
|
||
|
|
nextflow.enable.dsl = 2
|
||
|
|
|
||
|
|
include { SAMTOOLS_COLLATE } from '../../../../modules/samtools/collate/main.nf'
|
||
|
|
|
||
|
|
workflow test_samtools_collate {
|
||
|
|
|
||
|
|
input = [
|
||
|
|
[ id:'test', single_end:false ], // meta map
|
||
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
|
||
|
|
]
|
||
|
|
|
||
|
|
SAMTOOLS_COLLATE ( input, [] )
|
||
|
|
}
|
||
|
|
|
||
|
|
workflow test_samtools_collate_cram {
|
||
|
|
|
||
|
|
input = [
|
||
|
|
[ id:'test', single_end:false ], // meta map
|
||
|
|
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)
|
||
|
|
]
|
||
|
|
|
||
|
|
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||
|
|
|
||
|
|
SAMTOOLS_COLLATE ( input, fasta )
|
||
|
|
}
|