Skip to content
Snippets Groups Projects
Commit 763ac90a authored by Venkat Malladi's avatar Venkat Malladi
Browse files

Fix config for references.

parent 15122e72
No related merge requests found
# Title to use for the report.
title: BICF ChIP-seq Analysis Report
report_comment: >
This report has been generated by the <a href="https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/" target="_blank">BICF/chipseq_analysis</a>
pipeline.
report_section_order:
software_versions:
order: -1000
report_section_order:
software_references:
order: -1000
extra_fn_clean_exts:
- '_R1'
- '_R2'
- 'pbc.qc'
fn_ignore_files:
- '*dedup.flagstat.qc'
custom_data:
library_complexity:
file_format: 'tsv'
id: 'library_complexity'
contents: 'TotalReadPairs DistinctReadPairs OneReadPair TwoReadPairs NRF PBC1 PBC2'
section_name: 'Library complexity'
plot_type: 'generalstats'
sp:
phantompeakqualtools/out:
fn: '*cc.qc'
library_complexity:
fn: '*pbc.qc'
......@@ -505,8 +505,8 @@ process softwareReport {
output:
file('*_mqc.yaml') into softwareVersions
file('*_mqc.txt') into softwareReferences
file('software_versions_mqc.yaml') into softwareVersions
file('software_references_mqc.yaml') into softwareReferences
script:
"""
......
......@@ -44,20 +44,21 @@ def main():
reference = args.reference
output = args.output
out_filename = output + '_mqc.txt'
out_filename = output + '_mqc.yaml'
# Header for HTML
print('''
# id: 'References'
# section_name: 'References'
# description: 'This section describes references for the tools used.'
# plot_type: 'html'
id: 'Software References'
section_name: 'Software References'
description: 'This section describes references for the tools used.'
plot_type: 'html'
data: |
'''
, file = open(out_filename, "w")
)
# Turn Markdown into HTML
references_html = 'bash -c "pandoc {} >> {}"'
references_html = 'bash -c "pandoc -p {} | sed \'s/^/ /\' >> {}"'
references_html = references_html.format(reference, out_filename)
subprocess.check_call(shlex.split(references_html))
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment