nf-core_modules/tests/software/trimgalore/main.nf

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { TRIMGALORE as TRIMGALORE_SE } from '../../../software/trimgalore/main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
include { TRIMGALORE as TRIMGALORE_PE } from '../../../software/trimgalore/main.nf' addParams( options: [ publish_dir:'test_paired_end' ] )
/*
* Test with single-end data
*/
workflow test_trimgalore_single_end {
def input = []
input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ]
TRIMGALORE_SE ( input )
}
// workflow test_trimgalore_single_end {
// def input = []
// input = [ [ id:'test', single_end:false ], // meta map
// [ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ]
// TRIMGALORE_SE ( input )
// }
/*
* Test with paired-end data
*/
workflow test_trimgalore_paired_end {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
TRIMGALORE_PE ( input )
}