fix: add apptainer source, yml formatting (#45)

* fix: add apptainer source, yml formatting

* fix: added apptainer installation to test wf, yaml formatting

Author: m-jahn

.github/workflows/main.yml

@@ -9,27 +9,27 @@ on:
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
-    
+
     steps:
-    - uses: actions/checkout@v1
+      - uses: actions/checkout@v4
+
+      - name: Test run
+        uses: ./
+        with:
+          directory: .test
+          snakefile: .test/Snakefile
+          args: "--cores 1"
 
-    - name: Test run
-      uses: ./
-      with:
-        directory: .test
-        snakefile: .test/Snakefile
-        args: "--cores 1"
+      - name: Test containerize
+        uses: ./
+        with:
+          directory: .test
+          snakefile: .test/Snakefile
+          install-apptainer: true
+          args: "--cores 1"
+          task: "containerize"
 
-    - name: Test containerize
-      uses: ./
-      with:
-        directory: .test
-        snakefile: .test/Snakefile
-        args: "--cores 1"
-        task: "containerize"
-  
-    - name: Show Dockerfile
-      run: |
-        cat Dockerfile
+      - name: Show Dockerfile
+        run: |
+          cat Dockerfile

action.yml

@@ -17,30 +17,30 @@ inputs:
   args:
     description: Additional Snakemake arguments to use
     required: false
-    default: ''
+    default: ""
   stagein:
     description: Additional steps to prepare the workflow for execution
     required: false
-    default: ''
+    default: ""
   task:
     description: Whether to run Snakemake or to generate a container image specification.
     required: false
-    default: 'run'
+    default: "run"
   show-disk-usage-on-error:
     description: Whether to return the used disk space on failing.
     required: false
     default: false
   snakemake-version:
     description: Snakemake version to use. If not specified, uses latest version. Pin a specific version (e.g., '8.25.5') for reproducibility.
     required: false
-    default: '*'
+    default: "*"
   install-apptainer:
     description: Install Apptainer (true/false)
     required: false
     default: false
 
 runs:
-  using: 'composite'
+  using: "composite"
   steps:
     - name: Validate inputs
       if: ${{ ! (inputs.task == 'containerize' || inputs.task == 'run' )}}
@@ -57,8 +57,10 @@ runs:
           echo "Error: This action currently supports Apptainer installation only on Ubuntu runners"
           exit 1
         fi
+        sudo add-apt-repository -y ppa:apptainer/ppa
         sudo apt-get update
         sudo apt-get install -y apptainer
+
     - name: Prepare .snakemake.environment.yaml
       shell: bash -el {0}
       run: |
@@ -104,4 +106,3 @@ runs:
       if: ${{ inputs.task == 'containerize' }}
       shell: bash -el {0}
       run: snakemake --directory ${{ inputs.directory }} --snakefile ${{ inputs.snakefile }} --show-failed-logs ${{ inputs.args }} --containerize > Dockerfile
-