From af7475c9b747843ee2d3d9e4626e5976eb2e3141 Mon Sep 17 00:00:00 2001
From: Matt Parker <matt.parker@nanoporetech.com>
Date: Mon, 21 Aug 2023 19:18:21 +0000
Subject: [PATCH] CW-2615: update data

---
 CHANGELOG.md         | 6 ++++++
 nextflow.config      | 8 ++++----
 nextflow_schema.json | 2 +-
 3 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 000352d..e504450 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,12 @@ 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).
 
+## [v0.3.31]
+### Changed
+- `--update_data` default is now `true` to get latest lineage data from Pangolin and Nextclade
+### Updated
+- Pangolin and Nextclade containers update to latest data
+
 ## [v0.3.30]
 ### Added
 - New primer schemes; ARTIC V5.3.2 and Midnight IDT V2
diff --git a/nextflow.config b/nextflow.config
index 554d28e..92eb299 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -39,7 +39,7 @@ params {
     pangolin_options = null
     nextclade_data_tag = null
     nextclade_version = "2.14.0"
-    update_data = false
+    update_data = true
     aws_image_prefix = null
     aws_queue = null
     disable_ping = false
@@ -60,8 +60,8 @@ params {
         ]
         common_sha = "sha0fa3896acb70eecc0d432c91a1516d596a87741c"
         container_sha = 'shaa5485f2d1c9085c23b266273556a4ce01e5e0dd9'
-        nextclade_sha = 'sha24df77bfdb05353178d9798d1edf87822ae84756'
-        pangolin_sha = 'sha983ccbd03506597918e5c99689eac6fcc84de431'
+        nextclade_sha = 'shae56aff3b5b498b8cb950993692f914033397f8da'
+        pangolin_sha = 'shae304dd3bc308a519f26908eb9d5ffa7686131d17'
     }
 }
 
@@ -72,7 +72,7 @@ manifest {
     description     = 'Run the ARTIC SARS-CoV-2 methodology on multiplexed MinION, GridION, and PromethION data.'
     mainScript      = 'main.nf'
     nextflowVersion = '>=23.04.2'
-    version         = 'v0.3.30'
+    version         = 'v0.3.31'
 }
 
 epi2melabs {
diff --git a/nextflow_schema.json b/nextflow_schema.json
index dc2fdc9..0eb77e8 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -221,7 +221,7 @@
                 },
                 "update_data": {
                     "type": "boolean",
-                    "default": false,
+                    "default": true,
                     "description": "Update Pangolin and Nextclade data at runtime."
                 },
                 "pangolin_options": {