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Merged
ahmig merged 4 commits into from
Apr 14, 2026
Merged

ci: remove test with Snakemake v8 #44

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9d1d175
ci: remove test with Snakemake v8
ahmig Apr 14, 2026
a5ba554
ci: update Snakemake v9 minor for tests
ahmig Apr 14, 2026
a69e34c
ci: update Snakemake v9 for apptainer test
ahmig Apr 14, 2026
8112b11
docs: update Snakemake versions on README
ahmig Apr 14, 2026
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39 changes: 0 additions & 39 deletions .github/workflows/test_v8.yml
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2 changes: 1 addition & 1 deletion .test/environment_apptainer.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,5 +5,5 @@ channels:
- defaults
dependencies:
- python==3.11.6
- snakemake==9.1.6
- snakemake==9.15.0
- apptainer==1.4.1
8 changes: 0 additions & 8 deletions .test/environment_v8.yaml
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2 changes: 1 addition & 1 deletion .test/environment_v9.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,4 +5,4 @@ channels:
- defaults
dependencies:
- python==3.11.6
- snakemake==9.1.6
- snakemake==9.15.0
5 changes: 2 additions & 3 deletions README.md
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Expand Up @@ -11,7 +11,6 @@

![Install workflow](https://github.com/PathoGenOmics-Lab/VIPERA/actions/workflows/install.yml/badge.svg)
![Test workflow with Snakemake v7](https://github.com/PathoGenOmics-Lab/VIPERA/actions/workflows/test_v7.yml/badge.svg)
![Test workflow with Snakemake v8](https://github.com/PathoGenOmics-Lab/VIPERA/actions/workflows/test_v8.yml/badge.svg)
![Test workflow with Snakemake v9](https://github.com/PathoGenOmics-Lab/VIPERA/actions/workflows/test_v9.yml/badge.svg)
![Test workflow with Snakemake v9 and Apptainer](https://github.com/PathoGenOmics-Lab/VIPERA/actions/workflows/test_apptainer.yml/badge.svg)

Expand Down Expand Up @@ -42,8 +41,8 @@ It supports dependency management through either conda or Apptainer/Singularity,

We use continuous integration (CI) to automatically verify that all dependencies install correctly
with Snakemake v7.32.4 (see GitHub Action `Install`), and to test that VIPERA runs
successfully with Snakemake v7.32.4, v8.30.0, and v9.1.6 using conda (Actions `Test Sm v[7-9]`).
We also test a containerized workflow with Snakemake v9.1.6 and Apptainer using a
successfully with Snakemake v7.32.4 and v9.15.0 using conda (Actions `Test Sm v(7|9)`).
We also test a containerized workflow with Snakemake v9.15.0 and Apptainer using a
[remote image](https://hub.docker.com/r/ahmig/vipera) (Action `Test Sm v9 Apptainer`).
This image is automatically updated in every version (Action `Deploy`).

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