nf-core_modules/tests/software/bwa/main.nf
2021-02-02 12:35:06 +00:00

42 lines
1.4 KiB
Text

#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { BWA_INDEX } from '../../../software/bwa/index/main.nf' addParams( options: [:] )
include { BWA_MEM as BWA_MEM_SE } from '../../../software/bwa/mem/main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
include { BWA_MEM as BWA_MEM_PE } from '../../../software/bwa/mem/main.nf' addParams( options: [ publish_dir:'test_paired_end' ] )
workflow test_bwa_index {
BWA_INDEX ( file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) )
}
/*
* Test with single-end data
*/
workflow test_bwa_mem_single_end {
def input = []
input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz", checkIfExists: true) ] ]
BWA_MEM_SE (
input,
file("${launchDir}/tests/data/index/E_coli/bwa/", checkIfExists: true)
)
}
/*
* Test with paired-end data
*/
workflow test_bwa_mem_paired_end {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R2.fastq.gz", checkIfExists: true) ] ]
BWA_MEM_PE (
input,
file("${launchDir}/tests/data/index/E_coli/bwa/", checkIfExists: true)
)
}