Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

feat!: Use composite action with conda instead of docker action #39

Open
wants to merge 17 commits into
base: master
Choose a base branch
from
Open
Show file tree
Hide file tree
Changes from 15 commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 0 additions & 4 deletions Dockerfile

This file was deleted.

80 changes: 70 additions & 10 deletions action.yml
Original file line number Diff line number Diff line change
Expand Up @@ -27,17 +27,77 @@ 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: Snakemake version to use. If not specified, uses latest version. Pin a specific version (e.g., '8.25.5') for reproducibility.
required: false
default: '*'
Comment on lines +33 to +36
Copy link

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

⚠️ Potential issue

Fix invalid conda version specifier

The default value '*' is not a valid version specifier for conda packages. When this default is used, the environment creation will fail because the conda dependency specification snakemake ==* is invalid.

Consider these options:

  1. Remove the default value entirely to use the latest version
  2. Use a specific version as default (e.g., '8.25.5')

install-apptainer:
description: Install Apptainer (true/false)
required: false
default: false

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:
- 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

- name: Install Apptainer
if: ${{ inputs.install-apptainer == 'true' }}
shell: bash -el {0}
run: |
sudo apt-get update
sudo apt-get install -y apptainer

johanneskoester marked this conversation as resolved.
Show resolved Hide resolved
- name: Prepare .snakemake.environment.yaml
shell: bash -el {0}
run: |
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
with:
channels: conda-forge,bioconda
channel-priority: strict
miniforge-version: latest
environment-file: .snakemake.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}
run: |
snakemake --directory ${{ inputs.directory }} --snakefile ${{ inputs.snakefile }} --show-failed-logs ${{ inputs.args }}
Copy link

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

🛠️ Refactor suggestion

Quote paths to handle spaces and special characters

The directory and snakefile paths should be quoted to handle spaces and special characters correctly.

-        snakemake --directory ${{ inputs.directory }} --snakefile ${{ inputs.snakefile }} --show-failed-logs ${{ inputs.args }}
+        snakemake --directory "${{ inputs.directory }}" --snakefile "${{ inputs.snakefile }}" --show-failed-logs ${{ inputs.args }}
-      run: snakemake --directory ${{ inputs.directory }} --snakefile ${{ inputs.snakefile }} --show-failed-logs ${{ inputs.args }} --containerize > Dockerfile
+      run: snakemake --directory "${{ inputs.directory }}" --snakefile "${{ inputs.snakefile }}" --show-failed-logs ${{ inputs.args }} --containerize > Dockerfile

Also applies to: 105-105

if [[ "$?" -ne 0 ]]; then
if [[ ${{ inputs.show-disk-usage-on-error }} = true ]]; then
# return disk usage and space on failing
df -h
printf "disk usage working directory"
du -h -d3 ${{ inputs.directory }}
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
johanneskoester marked this conversation as resolved.
Show resolved Hide resolved

25 changes: 0 additions & 25 deletions entrypoint.sh

This file was deleted.

6 changes: 6 additions & 0 deletions environment.yaml.template
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
channels:
- conda-forge
- bioconda
- nodefaults
dependencies:
- snakemake =={{ snakemake_version }}
Loading