nf-core_modules/tests/modules/picard/collectmultiplemetrics/main.nf
Adam Talbot 43d05d5482
fix (1852): picard/collectmultiplemetrics supports CRAM (#1853)
* 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
2022-07-06 19:05:53 +02:00

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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 )
}