nf-core_modules/software/bwa/mem/test/main.nf
2020-08-07 13:24:24 +01:00

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { BWA_MEM } from '../main.nf'
/*
* Test with single-end data
*/
workflow test_single_end {
def input = []
input = [ [ id:'test', single_end:true ], // meta map
[ file("${baseDir}/input/Ecoli_DNA_R1.fastq.gz", checkIfExists: true) ] ]
BWA_MEM (
input,
file("${baseDir}/input/index/NC_010473.fa.{amb,ann,bwt,pac,sa}", checkIfExists: true),
file("${baseDir}/input/NC_010473.fa", checkIfExists: true),
[ publish_dir:'test_paired_end' ]
)
}
/*
* Test with paired-end data
*/
workflow test_paired_end {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
[ file("${baseDir}/input/Ecoli_DNA_R1.fastq.gz", checkIfExists: true),
file("${baseDir}/input/Ecoli_DNA_R2.fastq.gz", checkIfExists: true) ] ]
BWA_MEM (
input,
file("${baseDir}/input/index/NC_010473.fa.{amb,ann,bwt,pac,sa}", checkIfExists: true),
file("${baseDir}/input/NC_010473.fa", checkIfExists: true),
[ publish_dir:'test_paired_end' ]
)
}
workflow {
test_single_end()
test_paired_end()
}