Commit 2d250508 authored by Lukas Jelonek's avatar Lukas Jelonek
Browse files

Add multiqc step

parent e7e81203
#!/usr/bin/env nextflow
params.location = 's3://lj-nf-fastq-testdata/data/*.fastq.gz'
Channel.fromPath(params.location).set{ch_fastqs}
params.publish = 's3://lj-nf-fastq-testdata/results/'
Channel.fromPath(params.location).into{ch_fastqs1}
process run_fastqc {
publishDir params.publish
process debug_print_file_name {
echo true
input:
file f from ch_fastqs
file f from ch_fastqs1
output:
file "*.zip" into ch_qc_reports
script:
"""
fastqc $f
"""
}
process run_multiqc {
publishDir params.publish
input:
file f from ch_qc_reports.collect()
output:
file "multiqc*" into ch_multiqc_result
script:
"""
echo $f
multiqc $f
"""
}
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