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