mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
e726b1730d
* MD finally supports cram output * publish crai file * fix test output * fix mv * figure out if contains breaks stuff * remove variable checksum * add contains check * remove variable checksum Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
34 lines
1.5 KiB
Text
34 lines
1.5 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { GATK4_MARKDUPLICATES } from '../../../../modules/gatk4/markduplicates/main.nf'
|
|
include { GATK4_MARKDUPLICATES as GATK4_MARKDUPLICATES_CRAM } from '../../../../modules/gatk4/markduplicates/main.nf'
|
|
|
|
workflow test_gatk4_markduplicates {
|
|
input = [ [ id:'test', single_end:false ], // meta map
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
|
|
]
|
|
|
|
GATK4_MARKDUPLICATES ( input, [], [] )
|
|
}
|
|
|
|
workflow test_gatk4_markduplicates_multiple_bams {
|
|
input = [ [ id:'test', single_end:false ], // meta map
|
|
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
|
|
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)
|
|
] ]
|
|
|
|
GATK4_MARKDUPLICATES ( input, [], [] )
|
|
}
|
|
|
|
workflow test_gatk4_markduplicates_multiple_cram_output {
|
|
input = [ [ id:'test', single_end:false ], // meta map
|
|
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
|
|
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], 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)
|
|
|
|
GATK4_MARKDUPLICATES_CRAM ( input, fasta, fai )
|
|
}
|