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31166227d3
* Separate MultiQC config from logo input channel * Update meta.yml * Update main.nf * Add test for new check * md5sum -> contains
45 lines
1.4 KiB
Text
45 lines
1.4 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { FASTQC } from '../../../modules/fastqc/main.nf'
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include { FASTQC as FASTQC2 } from '../../../modules/fastqc/main.nf'
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include { MULTIQC } from '../../../modules/multiqc/main.nf'
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workflow test_multiqc {
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input = [
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[ id: 'test', single_end: false ],
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[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
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]
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FASTQC ( input )
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MULTIQC ( FASTQC.out.zip.collect { it[1] }, [],[] )
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}
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workflow test_multiqc_fn_collision {
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fqc_input = [
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[ id: 'test', single_end: false ],
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[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
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]
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mqc_input = Channel.empty()
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FASTQC ( fqc_input )
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mqc_input = mqc_input.mix(FASTQC.out.zip.collect { it[1] })
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FASTQC2 ( fqc_input )
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mqc_input = mqc_input.mix(FASTQC2.out.zip.collect { it[1] })
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MULTIQC ( mqc_input, [],[] )
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}
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workflow test_multiqc_config {
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input = [
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[ id: 'test', single_end: false ],
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[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
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]
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mqc_config = file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)
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mqc_input = Channel.empty()
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FASTQC ( input )
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MULTIQC ( FASTQC.out.zip.collect { it[1] }, mqc_config,[] )
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}
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