2019-12-05 14:57:32 +00:00
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#!/usr/bin/env nextflow
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2019-12-05 21:11:12 +00:00
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nextflow.preview.dsl = 2
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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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params.out_dir = "test_output"
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2020-03-16 14:17:38 +00:00
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params.fastqc_args = ''
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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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2020-03-16 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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2020-07-14 15:38:20 +00:00
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/**
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* Test if FASTQC runs with single-end data
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*/
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workflow test_single_end {
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input_files = Channel.fromPath("data/test_single_end.fastq.gz")
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2020-07-15 11:00:10 +00:00
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.map {f -> [f.baseName, true, f]}
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2020-07-14 15:38:20 +00:00
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FASTQC(input_files)
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}
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/**
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* Test if FASTQC runs with paired end data
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*/
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workflow test_paired_end {
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input_files = Channel.fromFilePairs("data/test_R{1,2}.fastq.gz")
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2020-07-15 11:00:10 +00:00
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.map {f -> [f[0], false, f[1]]}
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2020-07-14 15:38:20 +00:00
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FASTQC(input_files)
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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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