From 98c6d9ddcdfa05a3198f7d884b11e265c68315f1 Mon Sep 17 00:00:00 2001
From: Matt Parker <matt.parker@nanoporetech.com>
Date: Wed, 1 Dec 2021 14:25:55 +0000
Subject: [PATCH] adding check for internet connectivity

---
 CHANGELOG.md |  4 ++++
 main.nf      | 11 ++++++++++-
 2 files changed, 14 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 22d6bb4..c3b3101 100644
--- 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).
 
+## [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)
diff --git a/main.nf b/main.nf
index 32ac9d5..5618f5c 100644
--- a/main.nf
+++ b/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
     """