Merge branch 'CW-2503-update-pangolin-nextclade' into 'dev'

CW-2503 - update pangolin & nextclade Closes CW-2503 See merge request epi2melabs/workflows/wf-artic!145
epi2me-labs · Aug 1, 2023 · cab982c · cab982c
2 parents d83cbd5 + be0b3e0
commit cab982c
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,7 +8,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 - New primer schemes; ARTIC V5.3.2 and Midnight IDT V2
 ### Updated
-- Nextclade & pangolin
+- Nextclade bump to 2.14.0
+- Pangolin bump to 4.3
 - For alt primers we take the largest region (Updated ARTIC code merges a canonical primer site with an alt site, producing an interval that encompasses both)
 
 ## [v0.3.29]

diff --git a/main.nf b/main.nf
@@ -353,6 +353,9 @@ process pangolin {
     then
       pangolin --update
     fi
+    
+    # set cache for snakemake to prevent permission issuses
+    export XDG_CACHE_HOME=\$(pwd -P)
 
     pangolin --all-versions 2>&1 | sed 's/: /,/' > pangolin.version
     pangolin --threads ${task.cpus} $params._pangolin_options consensus.fasta

diff --git a/nextflow.config b/nextflow.config
@@ -36,10 +36,9 @@ params {
     report_lineage = true
     report_coverage = true
     report_variant_summary = true
-    pangolin_version = "4.2"
     pangolin_options = null
-    nextclade_version = "2.11.0"
     nextclade_data_tag = null
+    nextclade_version = "2.14.0"
     update_data = false
     aws_image_prefix = null
     aws_queue = null
@@ -61,8 +60,8 @@ params {
         ]
         common_sha = "sha0fa3896acb70eecc0d432c91a1516d596a87741c"
         container_sha = 'shaa5485f2d1c9085c23b266273556a4ce01e5e0dd9'
-        nextclade_sha = 'shaede3ca9a1b17c2a1d0696ef7ff8503ec167d5df9'
-        pangolin_sha = 'sha1266e6040bf6e9f02e569f0eba5011a17d47f7aa'
+        nextclade_sha = 'sha24df77bfdb05353178d9798d1edf87822ae84756'
+        pangolin_sha = 'sha983ccbd03506597918e5c99689eac6fcc84de431'
     }
 }
 

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -219,18 +219,13 @@
                     "default": false,
                     "description": "Update pangolin & Nextclade data at runtime."
                 },
-                "pangolin_version": {
-                    "type": "string",
-                    "default": "4.2",
-                    "hidden": true
-                },
                 "pangolin_options": {
                     "type": "string",
                     "description": "Pass options to pangolin, use like this \"--analysis-mode fast --min-length 26000\"."
                 },
                 "nextclade_version": {
                     "type": "string",
-                    "default": "2.11.0",
+                    "default": "2.14.0",
                     "hidden": true
                 },
                 "nextclade_data_tag": {