Merge branch 'pangolin-fix' into 'dev'

Pangolin fix See merge request epi2melabs/workflow-containers/wf-artic!80
epi2me-labs · Dec 2, 2021 · 8d13aab · 8d13aab
2 parents 0b11dbb + 1007f51
commit 8d13aab
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Showing 6 changed files with 11 additions and 15 deletions.
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -20,4 +20,4 @@ release-pangolin:
         AUX_IMAGE_NAME: "pangolin"
         AUX_IMAGE_ENVFILE: "environment_pangolin.yaml"
         AUX_IMAGE_DOCKERFILE: "Dockerfile_pangolin"
-        AUX_IMAGE_TAG: "3.1.16"
+        AUX_IMAGE_TAG: "3.1.16-0.3.9"
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,10 @@ 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).
 
+## [v0.3.9]
+### Changes
+- Pangolin update now takes place at build stage, rather than during run
+
 ## [v0.3.8]
 ### Fixed
 - Nextclade data was out of date, now calls Omicron

diff --git a/Dockerfile_pangolin b/Dockerfile_pangolin
@@ -10,5 +10,7 @@ RUN \
     && fix-permissions $CONDA_DIR \
     && fix-permissions $HOME
 
+RUN pangolin --update
+
 USER $WF_UID
 WORKDIR $HOME
diff --git a/main.nf b/main.nf
@@ -334,16 +334,6 @@ process pangolin {
         path "lineage_report.csv", emit: report
         path "pangolin.version", emit: version
     """
-    # Check to see if the box running the workflow has internet connectivity
-    EXIT_CODE=0
-    wget -q --spider --timeout 10 http://nanoporetech.com || EXIT_CODE=\$?
-
-    if [ \${EXIT_CODE} -eq 0 ]; then
-        pangolin --update
-    else
-        echo "Offline"
-    fi
-    
     pangolin --all-versions 2>&1 | sed 's/: /,/' > pangolin.version
     pangolin consensus.fasta
     """

diff --git a/nextflow.config b/nextflow.config
@@ -28,8 +28,8 @@ params {
     report_coverage = true
     report_variant_summary = true
     report_detailed = false
-    wfversion = "v0.3.8"
-    pangolin_version = "3.1.16"
+    wfversion = "v0.3.9"
+    pangolin_version = "3.1.16-0.3.9"
     aws_image_prefix = null
     aws_queue = null
     lab_id = null

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -220,12 +220,12 @@
         },
         "wfversion": {
             "type": "string",
-            "default": "v0.3.8",
+            "default": "v0.3.9",
             "hidden": true
         },
         "pangolin_version": {
             "type": "string",
-            "default": "3.1.16",
+            "default": "3.1.16-0.3.9",
             "hidden": true
         },
         "_min_len": {