set snakefile location

Author: johanneskoester

.github/workflows/main.yml

@@ -14,3 +14,4 @@ jobs:
     - uses: ./
       with:
         directory: .test
+        snakefile: .test/Snakefile

README.md

@@ -13,6 +13,10 @@ This action runs Snakemake on the repository.
 
 **Required** The working directory to use. Default `.test`.
 
+### `snakefile`
+
+The Snakefile containing the workflow description. Default `Snakefile`.
+
 ### `args`
 
 Additional arguments to pass to Snakemake.

action.yml

@@ -5,6 +5,9 @@ inputs:
     description: Working directory for the execution
     required: true
     default: .test
+  snakefile:
+    description: Snakefile containing the workflow description
+    default: Snakefile
   args:
     description: Additional Snakemake arguments to use
     required: false
@@ -14,4 +17,5 @@ runs:
   image: 'Dockerfile'
   args:
     - ${{ inputs.directory }}
+    - ${{ inputs.snakefile }}
     - ${{ inputs.args }}

entrypoint.sh

@@ -2,5 +2,5 @@
 
 export PATH=/opt/conda/bin:$PATH
 
-snakemake --directory $1 $2
+snakemake --directory $1 --snakefile $2 $3