diff --git a/CHANGELOG.md b/CHANGELOG.md index 2506cd5..f56ee7d 100644 --- a/CHANGELOG.md +++ b/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 (nf-validation@1.1.3 and nf-iridanext@0.2.0) -## 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 diff --git a/modules/local/arborview.nf b/modules/local/arborview.nf index 4903b28..d07d425 100644 --- a/modules/local/arborview.nf +++ b/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) diff --git a/modules/local/phyml/main.nf b/modules/local/phyml/main.nf index b6148b1..d7cb3a9 100644 --- a/modules/local/phyml/main.nf +++ b/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) diff --git a/nextflow.config b/nextflow.config index 6805620..2755874 100644 --- a/nextflow.config +++ b/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' }