From 55e68f6c47fd595ec06e249f646c7610e418e203 Mon Sep 17 00:00:00 2001 From: Chris Wright Date: Thu, 17 Jun 2021 09:24:00 +0100 Subject: [PATCH] Fix report formatting --- bin/report.py | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/bin/report.py b/bin/report.py index 1cbad52..c5ceac0 100755 --- a/bin/report.py +++ b/bin/report.py @@ -112,6 +112,7 @@ def main(): section = report_doc.add_section() section.markdown(''' ### Read Quality control + This section displays basic QC metrics indicating read data quality. ''') # read length summary @@ -180,7 +181,9 @@ def main(): section = report_doc.add_section() section.markdown(""" -### Artic Analysis status The panel below lists samples which failed to produce +### Artic Analysis status + +The panel below lists samples which failed to produce results from the primary ARTIC analysis. Samples not listed here were analysed successfully, but may still contain inconclusive or invalid results. See the following sections for further indications of failed or inconclusive results. @@ -208,7 +211,9 @@ def main(): if not args.hide_coverage: section = report_doc.add_section() section.markdown(''' -### Genome coverage Plots below indicate depth of coverage from data used +### Genome coverage + +Plots below indicate depth of coverage from data used within the Artic analysis coloured by amplicon pool. Variant filtering during the ARTIC analysis mandates a minimum coverage of at least {}X at variant/genotyping loci for a call to be made. @@ -345,6 +350,7 @@ def main(): section = report_doc.add_section() section.markdown(''' ### Software versions + The table below highlights versions of key software used within the analysis. ''') req = [ @@ -358,6 +364,7 @@ def main(): section = report_doc.add_section() section.markdown(''' ### Workflow parameters + The table below highlights values of the main parameters used in this analysis. ''') df_params = load_params(args.params)