mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +00:00
44 lines
1.6 KiB
Text
44 lines
1.6 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("${launchDir}/tests/data/index/E_coli/bwa/NC_010473.fa.{amb,ann,bwt,pac,sa}", checkIfExists: true),
|
|
file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", 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("${launchDir}/tests/data/index/E_coli/bwa/NC_010473.fa.{amb,ann,bwt,pac,sa}", checkIfExists: true),
|
|
file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
|
|
)
|
|
}
|