mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-13 13:23:09 +00:00
acb1a12a56
* Re-organise all test data * Fix ECLint * Fix ECLint agaaainn * Now is not the time EClint
33 lines
1.3 KiB
Text
33 lines
1.3 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { BWAMEM2_INDEX } from '../../../../software/bwamem2/index/main.nf' addParams( options: [:] )
|
|
include { BWAMEM2_MEM } from '../../../../software/bwamem2/mem/main.nf' addParams( options: [:] )
|
|
|
|
/*
|
|
* Test with single-end data
|
|
*/
|
|
workflow test_bwamem2_mem_single_end {
|
|
input = [ [ id:'test', single_end:true ], // meta map
|
|
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ]
|
|
]
|
|
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
|
|
|
|
BWAMEM2_INDEX ( fasta )
|
|
BWAMEM2_MEM ( input, BWAMEM2_INDEX.out.index )
|
|
}
|
|
|
|
/*
|
|
* Test with paired-end data
|
|
*/
|
|
workflow test_bwamem2_mem_paired_end {
|
|
input = [ [ id:'test', single_end:false ], // meta map
|
|
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
|
|
file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ]
|
|
]
|
|
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
|
|
|
|
BWAMEM2_INDEX ( fasta )
|
|
BWAMEM2_MEM ( input, BWAMEM2_INDEX.out.index )
|
|
}
|