Commit d897760f authored by Lukas Jelonek's avatar Lukas Jelonek
Browse files

Rename input and output parameter. Fix published data to only include html files

parent 8e41193f
#!/usr/bin/env nextflow
params.location = 's3://lj-nf-fastq-testdata/data/*.fastq.gz'
params.publish = 's3://lj-nf-fastq-testdata/results/'
Channel.fromPath(params.location).set{ch_fastqs1}
params.input = "${baseDir}/example_data/*.fastq.gz"
params.output = 'results'
Channel.fromPath(params.input).set{ch_fastqs1}
process run_fastqc {
publishDir params.publish
publishDir params.output + '/fastqc-reports', pattern: '*.html', mode: 'copy'
input:
file f from ch_fastqs1
output:
file "*.zip" into ch_qc_reports
file "*.zip" into ch_qc_report_data
file "*.html" into ch_qc_reports
script:
"""
......@@ -21,13 +23,13 @@ process run_fastqc {
}
process run_multiqc {
publishDir params.publish
publishDir params.output + '/multiqc-report', mode: 'copy'
input:
file f from ch_qc_reports.collect()
file f from ch_qc_report_data.collect()
output:
file "multiqc*" into ch_multiqc_result
file "*.html" into ch_multiqc_report
script:
"""
......
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