Skip to content
GitLab
Menu
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
nextflow
read-quality-control
Commits
d897760f
Commit
d897760f
authored
Oct 10, 2018
by
Lukas Jelonek
Browse files
Rename input and output parameter. Fix published data to only include html files
parent
8e41193f
Changes
1
Hide whitespace changes
Inline
Side-by-side
main.nf
View file @
d897760f
#!/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_report
s
.collect()
file f from ch_qc_report
_data
.collect()
output:
file "
multiqc*
" into ch_multiqc_re
sul
t
file "
*.html
" into ch_multiqc_re
por
t
script:
"""
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment