Merge branch 'no-internet' into 'dev'

adding check for internet connectivity

See merge request epi2melabs/workflow-containers/wf-artic!75

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).
 
+## [unreleased]
+### Fixed
+- Pangolin update step now checks for internet connection
+
 ## [v0.3.6]
 ### Changes
 - Pangolin updated to 3.1.16 (Will now call B.1.1.529 successfully)

main.nf

@@ -334,7 +334,16 @@ process pangolin {
         path "lineage_report.csv", emit: report
         path "pangolin.version", emit: version
     """
-    pangolin --update
+    # 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
     """