mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 03:28:17 +00:00
a90332906b
* add mergebamalignment * fix test.yml * update to latest gatk4 version * Update software/gatk4/mergebamalignment/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/data/README.md Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/mergebamalignment/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/mergebamalignment/meta.yml * fixed unmapped/unaligned Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
16 lines
769 B
Text
16 lines
769 B
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { GATK4_MERGEBAMALIGNMENT } from '../../../../software/gatk4/mergebamalignment/main.nf' addParams( options: [:] )
|
|
|
|
workflow test_gatk4_mergebamalignment {
|
|
def input = []
|
|
input = [ [ id:'test' ], // meta map
|
|
file("${launchDir}/tests/data/genomics/sarscov2/bam/test_single_end.bam", checkIfExists: true) ]
|
|
unmapped = file("${launchDir}/tests/data/genomics/sarscov2/bam/test_unaligned.bam", checkIfExists: true)
|
|
fasta = file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true)
|
|
dict = file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.dict", checkIfExists: true)
|
|
|
|
GATK4_MERGEBAMALIGNMENT ( input, unmapped, fasta, dict )
|
|
}
|