Merge branch 'cw-4813' into 'dev'

Update abricate container to use python3 [CW-4813]

See merge request epi2melabs/workflows/wf-flu!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).
 
+## [v1.2.2]
+### Changed
+- Updated abricate container to support EPI2ME Cloud, the version of abricate remains unchanged.
+
 ## [v1.2.1]
 ### Changed
 - Reconcile workflow with wf-template v5.2.5

nextflow.config

@@ -44,7 +44,7 @@ params {
 
         container_sha = "sha5eeb2cd0a75a6cc0f47d689d2926e0d9922ceda8"
         common_sha = "shae58638742cf84dbeeec683ba24bcdee67f64b986"
-        typing_sha = "shacd6e6b77d14424d746c3d7332dfa13e3bda9034f"
+        typing_sha = "sha671198c26ad22c97e3cdaa81a646ec0c215ebc43"
         medaka_sha = "sha3486abaab0d3b90351617eb8622acf2028edb154"
         nextclade_sha = "shab67652b34e898ec8dea18d0953a0b06b10466f76"
         agent = null
@@ -58,7 +58,7 @@ manifest {
     description     = 'Influenza A&B typing and analysis from Nanopore data.'
     mainScript      = 'main.nf'
     nextflowVersion = '>=23.04.2'
-    version         = 'v1.2.1'
+    version         = 'v1.2.2'
 }
 
 epi2melabs {
@@ -135,7 +135,7 @@ profiles {
                 memory = '2G'
             }
             withLabel:wfflutyping {
-                container = "${params.aws_image_prefix}-abricate:${params.wf.typing_sha}-root"
+                container = "${params.aws_image_prefix}-abricate:${params.wf.typing_sha}"
                 memory = '2G'
             }
             withLabel:nextclade {