From 763ac90a39a7092c08785a0444e01b573db36641 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Mon, 15 Apr 2019 11:23:22 -0500
Subject: [PATCH] Fix config for references.
---
workflow/conf/multiqc_config.yaml | 36 +++++++++++++++++++++++++
workflow/main.nf | 4 +--
workflow/scripts/generate_references.py | 13 ++++-----
3 files changed, 45 insertions(+), 8 deletions(-)
create mode 100644 workflow/conf/multiqc_config.yaml
diff --git a/workflow/conf/multiqc_config.yaml b/workflow/conf/multiqc_config.yaml
new file mode 100644
index 0000000..708ab12
--- /dev/null
+++ b/workflow/conf/multiqc_config.yaml
@@ -0,0 +1,36 @@
+# 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'
diff --git a/workflow/main.nf b/workflow/main.nf
index 7a1bed5..2526efc 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -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:
"""
diff --git a/workflow/scripts/generate_references.py b/workflow/scripts/generate_references.py
index 0b7582f..51be186 100644
--- a/workflow/scripts/generate_references.py
+++ b/workflow/scripts/generate_references.py
@@ -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))
--
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