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Add test

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This commit is contained in:
drpatelh 2020-08-07 11:31:07 +01:00
parent b1381bb577
commit 3a4fbf36ae
1 changed files with 27 additions and 7 deletions
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34
software/SOFTWARE/TOOL/test/main.nf
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@ -2,14 +2,34 @@
nextflow.enable.dsl = 2
include '../../../../tests/functions/check_process_outputs.nf' params(params)
include '../main.nf' params(params)
include { FASTQC } from '../main.nf'
reads = '../../../../test-datasets/tools/bwa/mem/reads/*_R{1,2}_001.fastq.gz'
index = '../../../../test-datasets/tools/bwa/mem/index/H3N2.{amb,ann,bwt,pac,sa}'
prefix = 'H3N2'
/*
* Test with single-end data
*/
workflow test_single_end {
def input = []
input = [ [ id:'test', single_end:true ], // meta map
[ file("${baseDir}/input/test_single_end.fastq.gz", checkIfExists: true) ] ]
FASTQC ( input, [ publish_dir:'test_single_end' ] )
}
/*
* Test with paired-end data
*/
workflow test_paired_end {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
[ file("${baseDir}/input/test_R1.fastq.gz", checkIfExists: true),
file("${baseDir}/input/test_R2.fastq.gz", checkIfExists: true) ] ]
FASTQC ( input, [ publish_dir:'test_paired_end' ] )
}
workflow {
read_input=Channel.fromFilePairs(reads)
bwa_mem(read_input,file(index),prefix)
test_single_end()
test_paired_end()
}