mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 03:28:17 +00:00
acb1a12a56
* Re-organise all test data * Fix ECLint * Fix ECLint agaaainn * Now is not the time EClint
30 lines
1.5 KiB
Text
30 lines
1.5 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { STRELKA_GERMLINE } from '../../../../software/strelka/germline/main.nf' addParams( options: [:] )
|
|
|
|
workflow test_strelka_germline {
|
|
input = [ [ id:'test'], // meta map
|
|
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true),
|
|
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam.bai", checkIfExists: true)
|
|
]
|
|
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
|
|
fai = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta.fai", checkIfExists: true)
|
|
targets = []
|
|
|
|
STRELKA_GERMLINE ( input, fasta, fai, targets )
|
|
}
|
|
|
|
workflow test_strelka_germline_target_bed {
|
|
input = [ [ id:'test'], // meta map
|
|
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true),
|
|
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam.bai", checkIfExists: true)
|
|
]
|
|
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
|
|
fai = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta.fai", checkIfExists: true)
|
|
targets = file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true)
|
|
|
|
STRELKA_GERMLINE ( input, fasta, fai, targets )
|
|
}
|
|
|