test

Author: jakevc

.github/workflows/main.yml

@@ -22,6 +22,14 @@ jobs:
         snakefile: .test/Snakefile
         args: "--cores 1"
 
+    - name: Test environment-file
+      uses: ./
+      with:
+        directory: .test
+        snakefile: .test/Snakefile
+        environment-file: .test/environment.yaml
+        args: "--cores 1"
+
     - name: Test containerize
       uses: ./
       with:

.test/environment.yaml

@@ -0,0 +1,6 @@
+channels:
+    - https://prefix.dev/conda-forge
+    - https://prefix.dev/bioconda
+    - nodefaults
+dependencies:
+    - snakemake ==5.9.0

action.yml

@@ -94,7 +94,7 @@ runs:
         channels: conda-forge,bioconda
         channel-priority: strict
         miniforge-version: latest
-        environment-file: ${{ inputs.environment-file != '' && inputs.environment-file || '.snakemake.environment.yaml' }}
+        environment-file: ${{ inputs.environment-file || '.snakemake.environment.yaml' }}
         activate-environment: snakemake
 
     - name: Display snakemake version