From a81f38fce6f3020192bc590b8c14481b6786c07a Mon Sep 17 00:00:00 2001
From: Till Hartmann <till.hartmann@bih-charite.de>
Date: Mon, 9 Dec 2024 11:38:27 +0100
Subject: [PATCH 01/17] feat: Use composite action instead of docker action

---
 Dockerfile                |  4 ----
 action.yml                | 47 ++++++++++++++++++++++++++++++---------
 entrypoint.sh             | 25 ---------------------
 environment.yaml.template |  6 +++++
 4 files changed, 43 insertions(+), 39 deletions(-)
 delete mode 100644 Dockerfile
 delete mode 100755 entrypoint.sh
 create mode 100644 environment.yaml.template

diff --git a/Dockerfile b/Dockerfile
deleted file mode 100644
index 67cdb03..0000000
--- a/Dockerfile
+++ /dev/null
@@ -1,4 +0,0 @@
-FROM snakemake/snakemake:stable
-COPY entrypoint.sh /entrypoint.sh
-ENV CONDA_ENVS_PATH /github/workspace/.conda
-ENTRYPOINT ["/entrypoint.sh"]
diff --git a/action.yml b/action.yml
index 84013b6..4d22178 100644
--- a/action.yml
+++ b/action.yml
@@ -27,17 +27,44 @@ inputs:
     required: false
     default: 'run'
   show-disk-usage-on-error:
-    descriptions: Whether to return the used disk space on failing.
+    description: Whether to return the used disk space on failing.
     required: false
     default: false
+  snakemake-version:
+   description: Which snakemake version to use
+   required: false
+   default: 8.25.5
 
 runs:
-  using: 'docker'
-  image: 'Dockerfile'
-  args:
-    - ${{ inputs.directory }}
-    - ${{ inputs.snakefile }}
-    - ${{ inputs.args }}
-    - ${{ inputs.stagein }}
-    - ${{ inputs.task }}
-    - ${{ inputs.show-disk-usage-on-error }}
+  using: 'composite'
+  steps:
+    - shell: bash -el {0}
+      run: sed 's/{{ snakemake_version }}/${{ inputs.snakemake-version }}/g' environment.yaml.template > environment.yaml
+    - name: Setup conda
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        channels: conda-forge,bioconda
+        channel-priority: strict
+        miniforge-version: latest
+        environment-file: environment.yaml
+    - name: Run snakemake
+      if: ${{ inputs.task == 'run' }}
+      shell: bash -el {0}
+      run: |
+        snakemake --directory ${{ inputs.directory }} --snakefile ${{ inputs.snakefile }} --show-failed-logs ${{ inputs.args }}
+        if [[ "$?" -ne 0 ]]; then
+          if [[ "$6" = true ]]; then
+              # return disk usage and space on failing
+              df -h
+              printf "disk usage working directory"
+              du -h -d3 $1
+          fi
+          exit 1
+      fi
+    - 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
+    - if: ${{ ! (inputs.task == 'containerize' || inputs.task == 'run' )}}
+      run: echo "Invalid value for 'task': '${{ inputs.task }}'. Options: 'containerize', 'run'." && exit 1
+
diff --git a/entrypoint.sh b/entrypoint.sh
deleted file mode 100755
index 668ad36..0000000
--- a/entrypoint.sh
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/bin/bash
-
-mkdir -p /github/workspace/.conda
-
-# run given stagein command
-eval "$4"
-
-# 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 $3
-    if [[ "$?" -ne 0 ]]; then
-        if [[ "$6" = true ]]; then
-            # return disk usage and space on failing
-            df -h
-            printf "disk usage working directory"
-            du -h -d3 $1
-        fi
-        exit 1
-    fi
-else
-    echo "Task input not recognized." && exit 1
-fi
diff --git a/environment.yaml.template b/environment.yaml.template
new file mode 100644
index 0000000..d6b4e2d
--- /dev/null
+++ b/environment.yaml.template
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - snakemake =={{ snakemake_version }}

From 34e5f691f728f19125299511041bb84013c87ee2 Mon Sep 17 00:00:00 2001
From: Till Hartmann <till.hartmann@bih-charite.de>
Date: Mon, 9 Dec 2024 11:40:58 +0100
Subject: [PATCH 02/17] fix indentation

---
 action.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/action.yml b/action.yml
index 4d22178..7c4517d 100644
--- a/action.yml
+++ b/action.yml
@@ -60,7 +60,7 @@ runs:
               du -h -d3 $1
           fi
           exit 1
-      fi
+        fi
     - name: Containerize snakemake
       if: ${{ inputs.task == 'containerize' }}
       shell: bash -el {0}

From 35f7d8ce213cdbf47f33e00b5ee96a4e76154d9a Mon Sep 17 00:00:00 2001
From: Till Hartmann <till.hartmann@bih-charite.de>
Date: Mon, 9 Dec 2024 11:42:55 +0100
Subject: [PATCH 03/17] swap quotes

---
 action.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/action.yml b/action.yml
index 7c4517d..6d565ae 100644
--- a/action.yml
+++ b/action.yml
@@ -66,5 +66,7 @@ runs:
       shell: bash -el {0}
       run: snakemake --directory ${{ inputs.directory }} --snakefile ${{ inputs.snakefile }} --show-failed-logs ${{ inputs.args }} --containerize > Dockerfile
     - if: ${{ ! (inputs.task == 'containerize' || inputs.task == 'run' )}}
-      run: echo "Invalid value for 'task': '${{ inputs.task }}'. Options: 'containerize', 'run'." && exit 1
+      run: |
+        echo 'Invalid value for "task": "${{ inputs.task }}". Options: "containerize", "run".'
+        exit 1
 

From 2551a815e7634c324973441dcad30f2be9a73d02 Mon Sep 17 00:00:00 2001
From: Till Hartmann <till.hartmann@bih-charite.de>
Date: Mon, 9 Dec 2024 11:44:10 +0100
Subject: [PATCH 04/17] include shell

---
 action.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/action.yml b/action.yml
index 6d565ae..deeace6 100644
--- a/action.yml
+++ b/action.yml
@@ -66,6 +66,7 @@ runs:
       shell: bash -el {0}
       run: snakemake --directory ${{ inputs.directory }} --snakefile ${{ inputs.snakefile }} --show-failed-logs ${{ inputs.args }} --containerize > Dockerfile
     - if: ${{ ! (inputs.task == 'containerize' || inputs.task == 'run' )}}
+      shell: bash -el {0}
       run: |
         echo 'Invalid value for "task": "${{ inputs.task }}". Options: "containerize", "run".'
         exit 1

From 786074daff6272e22b07903fc3df68d604fd690b Mon Sep 17 00:00:00 2001
From: Till Hartmann <till.hartmann@bih-charite.de>
Date: Mon, 9 Dec 2024 11:46:43 +0100
Subject: [PATCH 05/17] move check for containerize/run to top

---
 action.yml | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/action.yml b/action.yml
index deeace6..955abe8 100644
--- a/action.yml
+++ b/action.yml
@@ -38,6 +38,12 @@ inputs:
 runs:
   using: 'composite'
   steps:
+    - name: Validate inputs
+      if: ${{ ! (inputs.task == 'containerize' || inputs.task == 'run' )}}
+      shell: bash -el {0}
+      run: |
+        echo 'Invalid value for "task": "${{ inputs.task }}". Options: "containerize", "run".'
+        exit 1
     - shell: bash -el {0}
       run: sed 's/{{ snakemake_version }}/${{ inputs.snakemake-version }}/g' environment.yaml.template > environment.yaml
     - name: Setup conda
@@ -65,9 +71,4 @@ runs:
       if: ${{ inputs.task == 'containerize' }}
       shell: bash -el {0}
       run: snakemake --directory ${{ inputs.directory }} --snakefile ${{ inputs.snakefile }} --show-failed-logs ${{ inputs.args }} --containerize > Dockerfile
-    - if: ${{ ! (inputs.task == 'containerize' || inputs.task == 'run' )}}
-      shell: bash -el {0}
-      run: |
-        echo 'Invalid value for "task": "${{ inputs.task }}". Options: "containerize", "run".'
-        exit 1
 

From d84999bbfa00c22c0d4fb627670fad1f5095df74 Mon Sep 17 00:00:00 2001
From: Till Hartmann <till.hartmann@bih-charite.de>
Date: Mon, 9 Dec 2024 11:50:51 +0100
Subject: [PATCH 06/17] check show-disk-usage-on-error

---
 action.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/action.yml b/action.yml
index 955abe8..b836aeb 100644
--- a/action.yml
+++ b/action.yml
@@ -59,7 +59,7 @@ runs:
       run: |
         snakemake --directory ${{ inputs.directory }} --snakefile ${{ inputs.snakefile }} --show-failed-logs ${{ inputs.args }}
         if [[ "$?" -ne 0 ]]; then
-          if [[ "$6" = true ]]; then
+          if [[ ${{ inputs.show-disk-usage-on-error }} = true ]]; then
               # return disk usage and space on failing
               df -h
               printf "disk usage working directory"

From eeb286cc1813ef60af3a76ae39d91ed64b8d482a Mon Sep 17 00:00:00 2001
From: Till Hartmann <till.hartmann@bih-charite.de>
Date: Mon, 9 Dec 2024 11:53:26 +0100
Subject: [PATCH 07/17] fix du for directory

---
 action.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/action.yml b/action.yml
index b836aeb..09931e6 100644
--- a/action.yml
+++ b/action.yml
@@ -63,7 +63,7 @@ runs:
               # return disk usage and space on failing
               df -h
               printf "disk usage working directory"
-              du -h -d3 $1
+              du -h -d3 ${{ inputs.directory }}
           fi
           exit 1
         fi

From 68b501bd07ce984472f69054e774b21121d7a1e8 Mon Sep 17 00:00:00 2001
From: Till Hartmann <till.hartmann@bih-charite.de>
Date: Mon, 9 Dec 2024 17:46:09 +0100
Subject: [PATCH 08/17] rename env to 'snakemake'

---
 action.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/action.yml b/action.yml
index 09931e6..9c6aad3 100644
--- a/action.yml
+++ b/action.yml
@@ -53,6 +53,7 @@ runs:
         channel-priority: strict
         miniforge-version: latest
         environment-file: environment.yaml
+        activate-environment: snakemake
     - name: Run snakemake
       if: ${{ inputs.task == 'run' }}
       shell: bash -el {0}

From 8ae899760389b50f7d94451ad9d8bdac0d8d47dd Mon Sep 17 00:00:00 2001
From: Till Hartmann <till.hartmann@tu-dortmund.de>
Date: Mon, 9 Dec 2024 17:50:42 +0100
Subject: [PATCH 09/17] Update action.yml

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
---
 action.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/action.yml b/action.yml
index 9c6aad3..a47c232 100644
--- a/action.yml
+++ b/action.yml
@@ -31,9 +31,8 @@ inputs:
     required: false
     default: false
   snakemake-version:
-   description: Which snakemake version to use
-   required: false
-   default: 8.25.5
+    description: Snakemake version to use. If not specified, uses latest version. Pin a specific version (e.g., '8.25.5') for reproducibility.
+    required: false
 
 runs:
   using: 'composite'

From 53479d3882abf21936ef928a67581b463f094cab Mon Sep 17 00:00:00 2001
From: Till Hartmann <till.hartmann@bih-charite.de>
Date: Mon, 9 Dec 2024 18:03:41 +0100
Subject: [PATCH 10/17] simply use '*' as default for snakemake version

---
 action.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/action.yml b/action.yml
index a47c232..1d330cf 100644
--- a/action.yml
+++ b/action.yml
@@ -33,6 +33,7 @@ inputs:
   snakemake-version:
     description: Snakemake version to use. If not specified, uses latest version. Pin a specific version (e.g., '8.25.5') for reproducibility.
     required: false
+    default: '*'
 
 runs:
   using: 'composite'
@@ -45,6 +46,7 @@ runs:
         exit 1
     - shell: bash -el {0}
       run: sed 's/{{ snakemake_version }}/${{ inputs.snakemake-version }}/g' environment.yaml.template > environment.yaml
+
     - name: Setup conda
       uses: conda-incubator/setup-miniconda@v3
       with:

From 8a08969e94a0ad2d0e4a6a8cdca4ba478467a9a7 Mon Sep 17 00:00:00 2001
From: Till Hartmann <till.hartmann@bih-charite.de>
Date: Mon, 9 Dec 2024 18:05:34 +0100
Subject: [PATCH 11/17] show installed snakemake version by default

---
 action.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/action.yml b/action.yml
index 1d330cf..f981a90 100644
--- a/action.yml
+++ b/action.yml
@@ -55,6 +55,9 @@ runs:
         miniforge-version: latest
         environment-file: environment.yaml
         activate-environment: snakemake
+    - name: Display snakemake version
+      shell: bash -el {0}
+      run: snakemake --version
     - name: Run snakemake
       if: ${{ inputs.task == 'run' }}
       shell: bash -el {0}

From 991091fbba987356f4ab6e77fc520c086cf6fdea Mon Sep 17 00:00:00 2001
From: Till Hartmann <till.hartmann@bih-charite.de>
Date: Mon, 9 Dec 2024 18:08:53 +0100
Subject: [PATCH 12/17] add apptainer installation option

---
 action.yml | 17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 1 deletion(-)

diff --git a/action.yml b/action.yml
index f981a90..0d0f93f 100644
--- a/action.yml
+++ b/action.yml
@@ -34,6 +34,10 @@ inputs:
     description: Snakemake version to use. If not specified, uses latest version. Pin a specific version (e.g., '8.25.5') for reproducibility.
     required: false
     default: '*'
+  install-apptainer:
+    description: Install Apptainer (true/false)
+    required: false
+    default: false
 
 runs:
   using: 'composite'
@@ -44,7 +48,15 @@ runs:
       run: |
         echo 'Invalid value for "task": "${{ inputs.task }}". Options: "containerize", "run".'
         exit 1
-    - shell: bash -el {0}
+
+    - name: Install Apptainer
+      if: ${{ inputs.install-apptainer == 'true' }}
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y apptainer
+
+    - name: Prepare environment.yaml
+      shell: bash -el {0}
       run: sed 's/{{ snakemake_version }}/${{ inputs.snakemake-version }}/g' environment.yaml.template > environment.yaml
 
     - name: Setup conda
@@ -55,9 +67,11 @@ runs:
         miniforge-version: latest
         environment-file: environment.yaml
         activate-environment: snakemake
+
     - name: Display snakemake version
       shell: bash -el {0}
       run: snakemake --version
+
     - name: Run snakemake
       if: ${{ inputs.task == 'run' }}
       shell: bash -el {0}
@@ -72,6 +86,7 @@ runs:
           fi
           exit 1
         fi
+
     - name: Containerize snakemake
       if: ${{ inputs.task == 'containerize' }}
       shell: bash -el {0}

From 861c528bda7dc43bbffa95eaef95d3c26ecca990 Mon Sep 17 00:00:00 2001
From: Till Hartmann <till.hartmann@bih-charite.de>
Date: Mon, 9 Dec 2024 18:10:09 +0100
Subject: [PATCH 13/17] =?UTF-8?q?add=20missing=20'shell:=20=E2=80=A6'?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 action.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/action.yml b/action.yml
index 0d0f93f..01db76b 100644
--- a/action.yml
+++ b/action.yml
@@ -51,6 +51,7 @@ runs:
 
     - name: Install Apptainer
       if: ${{ inputs.install-apptainer == 'true' }}
+      shell: bash -el {0}
       run: |
         sudo apt-get update
         sudo apt-get install -y apptainer

From 8c55e2b266498a031a016a1659b4b40e224ecc85 Mon Sep 17 00:00:00 2001
From: Till Hartmann <till.hartmann@tu-dortmund.de>
Date: Tue, 10 Dec 2024 13:52:30 +0100
Subject: [PATCH 14/17] use here string

---
 action.yml | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/action.yml b/action.yml
index 01db76b..0ae6c36 100644
--- a/action.yml
+++ b/action.yml
@@ -56,9 +56,17 @@ runs:
         sudo apt-get update
         sudo apt-get install -y apptainer
 
-    - name: Prepare environment.yaml
+    - name: Prepare .snakemake.environment.yaml
       shell: bash -el {0}
-      run: sed 's/{{ snakemake_version }}/${{ inputs.snakemake-version }}/g' environment.yaml.template > environment.yaml
+      run: |8
+        cat <<EOF > .snakemake.environment.yaml
+        channels:
+          - conda-forge
+          - bioconda
+          - nodefaults
+        dependencies:
+          - snakemake ==${{ inputs.snakemake-version }}
+        EOF
 
     - name: Setup conda
       uses: conda-incubator/setup-miniconda@v3
@@ -66,7 +74,7 @@ runs:
         channels: conda-forge,bioconda
         channel-priority: strict
         miniforge-version: latest
-        environment-file: environment.yaml
+        environment-file: .snakemake.environment.yaml
         activate-environment: snakemake
 
     - name: Display snakemake version

From 8d6dd0449330b5cad99d9b1ff69e0e187cd60e70 Mon Sep 17 00:00:00 2001
From: Till Hartmann <till.hartmann@tu-dortmund.de>
Date: Tue, 10 Dec 2024 13:53:57 +0100
Subject: [PATCH 15/17] I guess the yaml parser does not support |8 notation

---
 action.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/action.yml b/action.yml
index 0ae6c36..89fb0c0 100644
--- a/action.yml
+++ b/action.yml
@@ -58,7 +58,7 @@ runs:
 
     - name: Prepare .snakemake.environment.yaml
       shell: bash -el {0}
-      run: |8
+      run: |
         cat <<EOF > .snakemake.environment.yaml
         channels:
           - conda-forge

From dedc6dc3cec13d813258896645d60db1d1ea2e60 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20K=C3=B6ster?= <johannes.koester@tu-dortmund.de>
Date: Tue, 10 Dec 2024 15:34:05 +0100
Subject: [PATCH 16/17] Delete environment.yaml.template

---
 environment.yaml.template | 6 ------
 1 file changed, 6 deletions(-)
 delete mode 100644 environment.yaml.template

diff --git a/environment.yaml.template b/environment.yaml.template
deleted file mode 100644
index d6b4e2d..0000000
--- a/environment.yaml.template
+++ /dev/null
@@ -1,6 +0,0 @@
-channels:
-  - conda-forge
-  - bioconda
-  - nodefaults
-dependencies:
-  - snakemake =={{ snakemake_version }}

From cebcb23c87aa3a23efddff3f79b3a4bd143d4120 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20K=C3=B6ster?= <johannes.koester@tu-dortmund.de>
Date: Tue, 10 Dec 2024 15:34:39 +0100
Subject: [PATCH 17/17] Update action.yml

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
---
 action.yml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/action.yml b/action.yml
index 89fb0c0..b1c06bb 100644
--- a/action.yml
+++ b/action.yml
@@ -53,9 +53,12 @@ runs:
       if: ${{ inputs.install-apptainer == 'true' }}
       shell: bash -el {0}
       run: |
+        if ! command -v apt-get &> /dev/null; then
+          echo "Error: This action currently supports Apptainer installation only on Ubuntu runners"
+          exit 1
+        fi
         sudo apt-get update
         sudo apt-get install -y apptainer
-
     - name: Prepare .snakemake.environment.yaml
       shell: bash -el {0}
       run: |