From 82708790e786e7fb6436f0f4dccc37cbd3514ca5 Mon Sep 17 00:00:00 2001
From: m-jahn <jahn@mpusp.mpg.de>
Date: Fri, 24 Apr 2026 10:13:21 +0200
Subject: [PATCH 1/3] fix: added containerize args, closes #57

---
 README.md  |  9 +++++++++
 action.yml | 12 +++++++++++-
 2 files changed, 20 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 7b0e4a3..1bf6b4e 100644
--- a/README.md
+++ b/README.md
@@ -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"
 ```
diff --git a/action.yml b/action.yml
index 87742da..3070922 100644
--- a/action.yml
+++ b/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

From 440ca6a7c44878ea33c49d84c8c70ee348d547f8 Mon Sep 17 00:00:00 2001
From: m-jahn <jahn@mpusp.mpg.de>
Date: Fri, 24 Apr 2026 10:13:48 +0200
Subject: [PATCH 2/3] update date

---
 LICENSE | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/LICENSE b/LICENSE
index 91f00bb..4538a2b 100644
--- a/LICENSE
+++ b/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

From 0ea0798a94722d9dcac6507842df5be77eae965d Mon Sep 17 00:00:00 2001
From: m-jahn <jahn@mpusp.mpg.de>
Date: Fri, 24 Apr 2026 13:35:25 +0200
Subject: [PATCH 3/3] fix: review comment

---
 README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 1bf6b4e..2ea389d 100644
--- a/README.md
+++ b/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`
 
@@ -42,7 +42,7 @@ Whether to install Apptainer (true/false). Default `false`.
 
 ### `containerize-args`
 
-Additional arguments for `containerize`, can be one of 'dockerfile', 'apptainer' or '' (defaults to dockerfile)
+Additional arguments for `containerize`, can be one of 'dockerfile', 'apptainer' or '' (defaults to dockerfile).
 
 ## Example usage