Merge branch 'handle-no-calls' into 'dev'

Ignore value errors from vcf fetch See merge request epi2melabs/workflow-containers/wf-artic!69
epi2me-labs · Nov 17, 2021 · 7101ea6 · 7101ea6
2 parents 1ca4e5a + fe98f99
commit 7101ea6
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,19 +4,15 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [unreleased]
-### Added
-- `--report_debug` flag to show additional coverage plots
-- Parsing of sample sheet to include a `type` column
-### Changes
-- `sample_name` changed to `sample_id` throughout
-
 ## [v0.3.5]
 ### Added
 - Error report if no data at all.
 - Telemetry JSON.
 - Nextclade errors output as seperate table.
-
+- `--report_debug` flag to show additional coverage plots
+- Parsing of sample sheet to include a `type` column
+### Changes
+- `sample_name` changed to `sample_id` throughout
 
 ## [v0.3.4]
 ### Added

diff --git a/bin/output_telemetry.py b/bin/output_telemetry.py
@@ -177,15 +177,18 @@ def build_telemetry(
                         primer[OVERLAP].append(per_base_count_alt)
 
                         # Cheekily grab calls from overlaps whilst we're at it
-                        for call in vcf.fetch(
-                                reference_name, base.pos-1, base.pos):
-                            primer[CALLS].append({
-                                POS: call.pos,
-                                QUAL: call.qual,
-                                REF: call.ref,
-                                ALT: call.alts,
-                                POOL: call.info.get('Pool')
-                            })
+                        try:
+                            for call in vcf.fetch(
+                                    reference_name, base.pos-1, base.pos):
+                                primer[CALLS].append({
+                                    POS: call.pos,
+                                    QUAL: call.qual,
+                                    REF: call.ref,
+                                    ALT: call.alts,
+                                    POOL: call.info.get('Pool')
+                                })
+                        except ValueError:
+                            pass
 
                 # Calculate additional summary stats
                 if per_base_count > 20:

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -221,7 +221,7 @@
         },
         "wfversion": {
             "type": "string",
-            "default": "v0.3.3",
+            "default": "v0.3.5",
             "hidden": true
         },
         "pangolin_version": {