nf-core_modules/tests/software/gatk4/applybqsr/main.nf
yocra3 614d61dc13
Add gatk4/applybqsr (#331)
* Add applybqsr module

* Solve problem in functions.nf

* Add to pytest
2021-03-23 14:15:26 +01:00

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1.6 KiB
Text

#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { GATK4_APPLYBQSR } from '../../../../software/gatk4/applybqsr/main.nf' addParams( options: [:] )
workflow test_gatk4_applybqsr {
def input = []
input = [ [ id:'test' ], // meta map
file("${launchDir}/tests/data/genomics/sarscov2/bam/test_paired_end.sorted.bam", checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/table/test.table", checkIfExists: true) ]
fasta = file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true)
fastaidx = file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta.fai", checkIfExists: true)
dict = file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.dict", checkIfExists: true)
GATK4_APPLYBQSR ( input, fasta, fastaidx, dict, [] )
}
workflow test_gatk4_applybqsr_intervals {
def input = []
input = [ [ id:'test' ], // meta map
file("${launchDir}/tests/data/genomics/sarscov2/bam/test_paired_end.sorted.bam", checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/table/test.table", checkIfExists: true) ]
fasta = file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true)
fastaidx = file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta.fai", checkIfExists: true)
dict = file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.dict", checkIfExists: true)
intervals = file("${launchDir}/tests/data/genomics/sarscov2/bed/test.bed", checkIfExists: true)
GATK4_APPLYBQSR ( input, fasta, fastaidx, dict, intervals)
}