mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-15 06:03:10 +00:00
43d05d5482
* fix (1852): picard/collectmultiplemetrics supports CRAM Changes: - Add .fai input to Picard CollectMultipleMetrics - Now supports CRAM effectively. - Will break existing pipelines! Fixes #1852 * 1852 Update meta.yml to include .fai
35 lines
1.4 KiB
Text
35 lines
1.4 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../../modules/picard/collectmultiplemetrics/main.nf'
|
|
|
|
workflow test_picard_collectmultiplemetrics {
|
|
input = [
|
|
[ id:'test', single_end:false ], // meta map
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
|
|
]
|
|
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
|
|
|
PICARD_COLLECTMULTIPLEMETRICS ( input, fasta, [] )
|
|
}
|
|
|
|
workflow test_picard_collectmultiplemetrics_nofasta {
|
|
input = [
|
|
[ id:'test', single_end:false ], // meta map
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
|
|
]
|
|
|
|
PICARD_COLLECTMULTIPLEMETRICS ( input, [], [] )
|
|
}
|
|
|
|
workflow test_picard_collectmultiplemetrics_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)
|
|
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
|
|
|
PICARD_COLLECTMULTIPLEMETRICS ( input, fasta, fai )
|
|
}
|