nf-core_modules/deprecated/multiqc/test/main.nf
2020-08-05 16:09:25 +01:00

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#!/usr/bin/env nextflow
nextflow.preview.dsl=2
params.outdir = "."
params.verbose = false
params.multiqc_args = ''
// include '../../../tests/functions/check_process_outputs.nf'
include '../main.nf'
if (params.verbose){
println ("[WORKFLOW] MULTIQC ARGS: " + params.multiqc_args)
}
multiqc_ch = Channel
.fromPath( ['../../../test-datasets/*trimming_report.txt','../../../test-datasets/*fastqc.zip','../../../test-datasets/*screen.txt','../../../test-datasets/*bowtie2_stats.txt'] )
.collect() // collect() flattens all channels to single list
// .view() // view the files in the channel
// Run the workflow
workflow {
main:
// This is an example workflow for real reads aligned with Bowtie2. Just for illustration purposes
// FASTQC (file_ch, params.outdir, params.fastqc_args, params.verbose)
// FASTQ_SCREEN (file_ch, params.outdir, params.fastq_screen_args, params.verbose)
// TRIM_GALORE (file_ch, params.outdir, params.trim_galore_args, params.verbose)
// FASTQC2 (TRIM_GALORE.out.reads, params.outdir, params.fastqc_args, params.verbose)
// BOWTIE2 (TRIM_GALORE.out.reads, params.outdir, params.bowtie2_args, params.verbose)
// merging channels for MultiQC
// multiqc_ch = FASTQC.out.report.mix(
// TRIM_GALORE.out.report,
// FASTQ_SCREEN.out.report,
// FASTQC2.out.report,
// BOWTIE2.out.stats,
// ).collect()
MULTIQC (multiqc_ch, params.outdir, params.multiqc_args, params.verbose)
// .check_output() TODO
}