Merge pull request #65 from MPUSP/dev

fix: added missing conf option

Author: m-jahn

.github/workflows/conventional-prs.yml

@@ -1,4 +1,3 @@
-name: Lint PR
 on:
   pull_request_target:
     types:
@@ -11,10 +10,5 @@ permissions:
   pull-requests: read
 
 jobs:
-  main:
-    name: Validate PR title
-    runs-on: ubuntu-latest
-    steps:
-      - uses: amannn/action-semantic-pull-request@v6
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  conventional-prs:
+    uses: MPUSP/mpusp-github-actions/.github/workflows/conventional-prs.yml@main

.github/workflows/deploy-apptainer.yml

@@ -0,0 +1,15 @@
+on:
+  workflow_run:
+    workflows: ["release-please"]
+    types:
+      - completed
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  packages: write
+
+jobs:
+  deploy-apptainer:
+    if: ${{ github.event_name == 'workflow_dispatch' || github.event.workflow_run.conclusion == 'success' }}
+    uses: MPUSP/mpusp-github-actions/.github/workflows/deploy-apptainer.yml@main

.github/workflows/deploy_apptainer.yml

@@ -1,20 +1,12 @@
 on:
   push:
-    branches:
-      - main
+    branches: [main]
 
 permissions:
   contents: write
   pull-requests: write
   issues: write
 
-name: release-please
-
 jobs:
   release-please:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: googleapis/release-please-action@v4
-        with:
-          token: ${{ secrets.GITHUB_TOKEN }}
-          release-type: go # just keep a changelog, no version anywhere outside of git tags
+    uses: MPUSP/mpusp-github-actions/.github/workflows/release-please.yml@main

.github/workflows/main.yml

@@ -0,0 +1,10 @@
+on:
+  pull_request:
+    branches: [main]
+
+jobs:
+  snakemake-tests:
+    uses: MPUSP/mpusp-github-actions/.github/workflows/snakemake-tests.yml@main
+    with:
+      cores: 2
+      dryrun: false

.github/workflows/release-please.yml

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2021, AUTHORS
+Copyright (c) 2026 Max Planck Unit for the Science of Pathogens
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

.github/workflows/snakemake-tests.yml

@@ -39,6 +39,7 @@ filter_guides:
   fiveprime_linker: Null
   threeprime_linker: Null
   export_as_gff: True
+  export_as_fasta: True
 
 report:
   show_examples: 20