Merge branch 'CW-3490' into 'dev'

CW-3490 - upgrade to nextclade v3

Closes CW-3490

See merge request epi2melabs/workflows/wf-artic!158

CHANGELOG.md

@@ -4,13 +4,19 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v1.1.0]
+### Updated
+- Nextclade updated to V3
+### Removed
+- Nextclade V2 datasets
+
 ## [v1.0.0]
-## Changes
+### Changes
 - Documentation
 - Defined resource requirments
 
 ## [v0.3.33]
-## Changes
+### Changes
 - Updates for cloud readiness
 - Docs updated
 ### Removed

bin/workflow_glue/report.py

@@ -286,17 +286,16 @@ def main(args):
             section=nextclade.NextClade(args.nextclade))
         section.markdown(
             "The table shows errors, warnings or failed genes per sample:")
-        error_df = pd.read_csv(args.nextclade_errors).fillna('None')
+        error_df = pd.read_csv(args.nextclade_errors, sep=";").fillna('None')
+        error_df = error_df[
+            ['index', 'seqName', 'clade', 'failedCdses', 'warnings', 'errors']]
         error_df.rename(
             columns={
                 'seqName': 'Sample Name',
-                'failedGenes': 'failed genes'}, inplace=True)
+                'warnings': 'Warnings',
+                'errors': 'Errors',
+                'failedCdses': 'Failed CDS'}, inplace=True)
         section.table(error_df, index=False)
-        section.markdown(
-            "*Note: For targeted sequencing, such as SpikeSeq, Nextclade "
-            "may report 'Missing data' QC fails. This is expected and not "
-            "a concern provided the regions of interest are not reported "
-            "as missing.*")
 
     # Pangolin analysis
     if args.pangolin is not None: