2019-12-05 14:57:32 +00:00
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#!/usr/bin/env nextflow
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2020-03-16 14:17:38 +00:00
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2020-08-06 23:35:34 +00:00
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nextflow.enable.dsl = 2
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params.outdir = "results/"
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2020-07-14 15:38:20 +00:00
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params.publish_dir_mode = "copy"
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2020-08-06 23:35:34 +00:00
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params.conda = false
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2020-03-16 14:17:38 +00:00
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2020-07-14 15:38:20 +00:00
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include { FASTQC } from '../main.nf'
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2019-12-05 14:57:32 +00:00
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2020-08-06 23:35:34 +00:00
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/*
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* Test with single-end data
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2020-07-14 15:38:20 +00:00
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*/
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workflow test_single_end {
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2020-07-16 12:20:37 +00:00
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2020-08-06 23:35:34 +00:00
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def reads = []
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reads = [ [ id:'test', single_end:true ],
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[ file('input/test_single_end.fastq.gz', checkIfExists: true) ] ]
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2020-07-16 12:20:37 +00:00
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2020-08-06 23:35:34 +00:00
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FASTQC ( reads, [:] )
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2020-07-14 15:38:20 +00:00
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}
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2020-08-06 23:35:34 +00:00
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/*
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* Test with paired-end data
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2020-07-14 15:38:20 +00:00
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*/
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workflow test_paired_end {
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2020-07-16 12:20:37 +00:00
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2020-08-06 23:35:34 +00:00
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def reads = []
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reads = [ [ id:'test', single_end:false ],
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[ file('input/test_R1.fastq.gz', checkIfExists: true), file('input/test_R2.fastq.gz', checkIfExists: true) ] ]
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2020-07-16 12:20:37 +00:00
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2020-08-06 23:35:34 +00:00
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FASTQC ( reads, [:] )
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2020-07-14 15:38:20 +00:00
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}
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2019-12-05 14:57:32 +00:00
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2019-12-05 21:11:12 +00:00
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workflow {
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2020-07-14 15:38:20 +00:00
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test_single_end()
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test_paired_end()
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2019-12-05 14:57:32 +00:00
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}
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