fix: containerize arguments (#58)

* fix: added containerize args, closes #57

* update date

* fix: review comment

Author: m-jahn

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2019 snakemake
+Copyright (c) 2019-2026 The Snakemake team
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -22,7 +22,7 @@ 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`.
+Whether to run Snakemake or to generate a container image specification (`Dockerfile`, `apptainer.def`) that contains all required environments. Can be either `run` or `containerize`. Default `run`.
 
 ### `show-disk-usage-on-error`
 
@@ -36,6 +36,14 @@ Snakemake version to install from conda. Default `*` (latest available version f
 
 Optional Snakemake git branch to install from `https://github.com/snakemake/snakemake`. If set, this takes precedence over `snakemake-version` and Snakemake is installed from source via pip.
 
+### `install-apptainer`
+
+Whether to install Apptainer (true/false). Default `false`.
+
+### `containerize-args`
+
+Additional arguments for `containerize`, can be one of 'dockerfile', 'apptainer' or '' (defaults to dockerfile).
+
 ## Example usage
 
 ```yaml
@@ -69,4 +77,5 @@ Optional Snakemake git branch to install from `https://github.com/snakemake/snak
     directory: ".test"
     snakefile: "workflow/Snakefile"
     task: "containerize"
+    containerize-args: "apptainer"
 ```

action.yml

@@ -45,6 +45,10 @@ inputs:
     description: Install Apptainer (true/false)
     required: false
     default: "false"
+  containerize-args:
+    description: Additional arguments for --containerize, can be one of 'dockerfile', 'apptainer' or '' (defaults to dockerfile)
+    required: false
+    default: ""
 
 runs:
   using: "composite"
@@ -117,4 +121,10 @@ runs:
     - name: Containerize snakemake
       if: ${{ inputs.task == 'containerize' }}
       shell: bash -el {0}
-      run: snakemake --directory ${{ inputs.directory }} --snakefile ${{ inputs.snakefile }} --show-failed-logs ${{ inputs.args }} --containerize > Dockerfile
+      run: |
+        if [[ "${{ inputs.containerize-args }}" == "apptainer" ]]; then
+          recipe="apptainer.def"
+        else
+          recipe="Dockerfile"
+        fi
+        snakemake --directory ${{ inputs.directory }} --snakefile ${{ inputs.snakefile }} --show-failed-logs ${{ inputs.args }} --containerize ${{ inputs.containerize-args }} > $recipe