feat: bring your own condarc

.github/workflows/main.yml

@@ -8,7 +8,7 @@ on:
     branches_ignore: []
 
 jobs:
-  build:
+  test:
 
     runs-on: ubuntu-latest
 
@@ -33,3 +33,17 @@ jobs:
     - name: Show Dockerfile
       run: |
         cat Dockerfile
+
+  test-condarc:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Test condarc-file
+      uses: ./
+      with:
+        directory: .test
+        snakefile: .test/Snakefile
+        condarc-file: .test/condarc.yaml
+        stagein: "conda list"
+        args: "--cores 1"

.test/condarc.yaml

@@ -0,0 +1,4 @@
+channel_alias: https://prefix.dev/
+always_yes: true
+show_channel_urls: true
+

README.md

@@ -28,6 +28,18 @@ Whether to run Snakemake or to generate a container image specification (in the
 
 Whether used disk space shall be printed if Snakemake fails. Can be either `true` or `false` (default: `false`).
 
+### `snakemake-version`
+
+Snakemake version to use. If not specified, uses latest version. Pin a specific version (e.g., '8.25.5') for reproducibility.
+
+### `install-apptainer`
+
+Install Apptainer (true/false)
+
+### `condarc-file`
+
+Path to a custom condarc file (e.g., 'etc/condarc.yaml')
+
 ## Example usage
 
 ```yaml
@@ -46,6 +58,7 @@ Whether used disk space shall be printed if Snakemake fails. Can be either `true
     args: '--cores 1 --sdm conda --conda-cleanup-pkgs cache'
     stagein: '' # additional preliminary commands to run (can be multiline)
     show-disk-usage-on-error: true
+    condarc-file: 'condarc.yaml'
 
 
 - name: Create container file

action.yml

@@ -38,6 +38,9 @@ inputs:
     description: Install Apptainer (true/false)
     required: false
     default: false
+  condarc-file:
+    description: Path to a custom condarc file for workflow action environment (e.g. '.condarc').
+    default: ''
 
 runs:
   using: 'composite'
@@ -59,17 +62,28 @@ runs:
         fi
         sudo apt-get update
         sudo apt-get install -y apptainer
+
     - name: Prepare .snakemake.environment.yaml
       shell: bash -el {0}
       run: |
         cat <<EOF > .snakemake.environment.yaml
         channels:
           - conda-forge
           - bioconda
-          - nodefaults
         dependencies:
           - snakemake ==${{ inputs.snakemake-version }}
         EOF
+
+    - name: Validate custom condarc file
+      if: ${{ inputs.condarc-file != '' }}
+      shell: bash -el {0}
+      run: |
+        if [[ -f "${{ inputs.condarc-file }}" ]]; then
+          echo "Using custom condarc file: ${{ inputs.condarc-file }}"
+        else
+          echo "Error: Custom condarc file '${{ inputs.condarc-file }}' not found"
+          exit 1
+        fi
 
     - name: Setup conda
       uses: conda-incubator/setup-miniconda@v3
@@ -78,6 +92,8 @@ runs:
         channel-priority: strict
         miniforge-version: latest
         environment-file: .snakemake.environment.yaml
+        conda-remove-defaults: "true"
+        condarc-file: ${{ inputs.condarc-file }}
         activate-environment: snakemake
 
     - name: Display snakemake version