Merge pull request #25 from phac-nml/dev

Change container registry and python version for arborview

CHANGELOG.md

@@ -3,26 +3,32 @@
 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).
 
-## 2.1.0 - 2024/07/09
+## [2.1.1] - 2024/08/21
+
+### `Changed`
+
+- Container registry for aborview switched from docker.io to quay.io/biocontainers (python:3.11.6 to python:3.12)
+
+## [2.1.0] - 2024/07/09
 
 ### `Added`
 
 - Support for including contextual metadata in the input samplesheet: See [PR 22](https://github.com/phac-nml/snvphylnfc/pull/22)
 - ArborView HTML app functionality for viewing dendograms with contextual metadata: See [PR 22](https://github.com/phac-nml/snvphylnfc/pull/22)
 
-## 2.0.2 - 2024/05/21
+## [2.0.2] - 2024/05/21
 
 ### `Added`
 
 - Support for compressed (GZIP-formatted) reference files.
 
-## 2.0.1 - 2024/02/23
+## [2.0.1] - 2024/02/23
 
 ### `Changed`
 
 - Pinned Nextflow plugins to specific versions ([email protected] and [email protected])
 
-## 2.0.0 - 2024/02/14
+## [2.0.0] - 2024/02/14
 
 ### `Added`
 
@@ -38,3 +44,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Fixed`
 
 ### `Dependencies`
+
+[2.1.1]: https://github.com/phac-nml/snvphylnfc/releases/tag/2.1.1
+[2.1.0]: https://github.com/phac-nml/snvphylnfc/releases/tag/2.1.0
+[2.0.2]: https://github.com/phac-nml/snvphylnfc/releases/tag/2.0.2
+[2.0.1]: https://github.com/phac-nml/snvphylnfc/releases/tag/2.0.1
+[2.0.0]: https://github.com/phac-nml/snvphylnfc/releases/tag/2.0.0

modules/local/arborview.nf

@@ -4,8 +4,8 @@ process ARBOR_VIEW {
     stageInMode 'copy' // Need to copy in arbor view html
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-    "docker.io/python:3.11.6" :
-    "docker.io/python:3.11.6" }"
+    "https://depot.galaxyproject.org/singularity/python%3A3.12" :
+    "biocontainers/python:3.12" }"
 
     input:
     tuple path(tree), path(metadata)

modules/local/phyml/main.nf

@@ -9,7 +9,7 @@ Please refer to the README for more information.
 */
 process PHYML {
     label 'process_low'
-    container = "quay.io/biocontainers/phyml:3.3.20211231--hee9e358_0"
+    container = "biocontainers/phyml:3.3.20211231--hee9e358_0"
 
     input:
     path(snvAlignment_phy)

nextflow.config

@@ -217,7 +217,7 @@ manifest {
     description     = """SNVPhyl Pipeline"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '2.1.0'
+    version         = '2.1.1'
     doi             = ''
     defaultBranch   = 'main'
 }