Add Apptainer action

Author: ahmig

.github/workflows/test_apptainer.yml

@@ -0,0 +1,39 @@
+name: Test Sm v9 Apptainer
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - main
+      - dev
+  pull_request:
+    branches:
+      - "**"
+
+jobs:
+  run_test_pipeline:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+      - name: Setup environment
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          channel-priority: strict
+          activate-environment: snakemake
+          auto-activate-base: false
+          miniforge-version: latest
+          environment-file: .test/environment_apptainer.yaml
+      - name: Run test pipeline
+        shell: bash -el {0}
+        run: snakemake --snakefile .test/Snakefile --configfile config/config.yaml .test/targets.yaml -c1 --sdm apptainer
+      - name: Pack logs
+        if: success() || failure()
+        shell: bash -el {0}
+        run: tar czf logs.tar.gz .test/output .snakemake/log
+      - name: Upload output file
+        if: success() || failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: output-logs
+          path: logs.tar.gz

.test/environment_apptainer.yaml

@@ -0,0 +1,9 @@
+name: snakemake
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - python==3.11.6
+  - snakemake==9.1.6
+  - apptainer==1.4.1

README.md

@@ -6,13 +6,13 @@
 
 [![PGO badge](https://img.shields.io/badge/PathoGenOmics-Lab-yellow.svg)](https://pathogenomics.github.io/)
 [![DOI](https://img.shields.io/badge/Virus_Evolution-10.1093/ve/veae018-387088.svg)](https://doi.org/10.1093/ve/veae018)
+[![Latest release](https://img.shields.io/github/v/release/PathoGenOmics-Lab/VIPERA)](https://github.com/PathoGenOmics-Lab/VIPERA/releases)
 
-[![Release](https://img.shields.io/github/v/release/PathoGenOmics-Lab/VIPERA)](https://github.com/PathoGenOmics-Lab/VIPERA/releases)
-[![Snakemake](https://img.shields.io/badge/Snakemake-≥7.19-brightgreen.svg?style=flat)](https://snakemake.readthedocs.io)
 ![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)
 
 A pipeline for SARS-CoV-2 Viral Intra-Patient Evolution Reporting and Analysis.