Merge pull request #14 from thomasbtf/containerize

feat: add containerize support

Author: johanneskoester

.github/workflows/main.yml

@@ -11,8 +11,22 @@ jobs:
 
     steps:
     - uses: actions/checkout@v1
-    - uses: ./
+
+    - name: Test run
+      uses: ./
+      with:
+        directory: .test
+        snakefile: .test/Snakefile
+        args: "--cores 1"
+
+    - name: Test containerize
+      uses: ./
       with:
         directory: .test
         snakefile: .test/Snakefile
         args: "--cores 1"
+        task: "containerize"
+  
+    - name: Show Dockerfile
+      run: |
+        cat Dockerfile

README.md

@@ -20,20 +20,31 @@ Additional arguments to pass to Snakemake.
 
 Preliminary commands to run before the workflow execution.
 
+### `task`
+
+Whether to run Snakemake or to generate a container image specification (in the form of a Dockerfile) that contains all required environments. Can be either `run` or `containerize`. Default `run`.
+
 ## Example usage
 
 ```yaml
 - name: Linting
-  uses: snakemake/snakemake-github-action@v1.19.0
+  uses: snakemake/snakemake-github-action@v1
   with:
     directory: '.test'
     snakefile: 'workflow/Snakefile'
     args: '--lint'
+
 - name: Testing
-  uses: snakemake/snakemake-github-action@v1.19.0
+  uses: snakemake/snakemake-github-action@v1
   with:
     directory: '.test'
     snakefile: 'workflow/Snakefile'
     args: '--cores 1 --use-conda --conda-cleanup-pkgs cache'
     stagein: '' # additional preliminary commands to run (can be multiline)
+
+- name: Create container file
+  uses: snakemake/snakemake-github-action@v1
+  with:
+    snakefile: 'workflow/Snakefile'
+    run: 'containerize'
 ```

action.yml

@@ -22,6 +22,10 @@ inputs:
     description: Additional steps to prepare the workflow for execution
     required: false
     default: ''
+  task:
+    description: Whether to run Snakemake or to generate a container image specification.
+    required: false
+    default: 'run'
 
 runs:
   using: 'docker'
@@ -31,3 +35,4 @@ runs:
     - ${{ inputs.snakefile }}
     - ${{ inputs.args }}
     - ${{ inputs.stagein }}
+    - ${{ inputs.task }}

entrypoint.sh

@@ -5,6 +5,12 @@ mkdir -p /github/workspace/.conda
 # run given stagein command
 eval "$4"
 
-# run snakemake with given args
-snakemake --directory $1 --snakefile $2 --show-failed-logs $3
-
+# create container file
+if [ "$5" = 'containerize' ] ; then
+    snakemake --directory $1 --snakefile $2 --show-failed-logs $3 --containerize > Dockerfile
+elif [ "$5" = 'run' ] ; then
+    # run snakemake with given args
+    snakemake --directory $1 --snakefile $2 --show-failed-logs $3
+else
+    echo "Task input not recognized." && exit 1
+fi