Containerization of workflow #112
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…pplementary workflow scripts
fix: split rules to separate dependencies
fix: split combined job to separate script-based job for better dependency management
ci: add supplementary scripts for container build process
…g list() to fix compatibility of root-paths
…conda or containers) fix: properly set the readline tabcompleter
…e snakemake_run_con object to properly access it from within workflows
…nakemake_run_conf object feat: add singularity arguments to snakemake config fix: pass the snakemak configuration settings in a dictionary to the snakemake workflow itself style: formatting with isort & black feat: handle the downloading of containers in the viroconstrictor wrapper
…nakemake_run_conf object feat: add singularity arguments to snakemake config for main workflow fix: pass the snakemake configuration settings in a dictionary to the main snakemake workflow itself feat: handle the downloading of containers necessary for main workflow in the viroconstrictor wrapper
chore: sync main to dev
Refactor the GitHub Actions workflows to update the triggers for container publishing. Change the trigger for the "build_and_test.yml" workflow to only run on pull requests to the main branch. Additionally, add a new workflow "publish_containers.yaml" to handle the publishing of containers. This workflow will be triggered on pushes to the dev branch. Related recent commits: - ci: change upstream registry - ci: temporarily add listing of directory contents for debugging purposes - ci: add step in container build/test workflow to download already existing containers
…omamba shell in GH actions
The `download_containers` function in the `containers.py` module has been refactored to include better error handling and logging. Previously, if a container failed to download, the function would return a non-zero status code without providing any specific error message. Now, when a container fails to download, the function logs an error message indicating the name of the container that failed. This change improves the clarity of error reporting and makes it easier to troubleshoot container download issues. Related recent commits: - refactor: add verbose option to `download_containers` function - ci: temporarily add listing of directory contents for debugging purposes - ci: add step in container build/test workflow to download already existing containers
Containerization of workflow
validate workflow runs
fix: pass correct configfile in main workflow in local execution fix: remove print statement leftover from debugging
…sed as reproducibility method
…T_SCORE. Check for a range instead of equality
…ction refactor: remove redundant comment
feat: add extra filtering options to clipper.py for future presets/usecases + adhoc alignment wrangling
…having a giant dict with all params
chore: sync main to dev
chore: sync main to dev
…o reflect the docker usage instead of apptainer
chore: sync main to dev
chore: sync main to dev
…were given (--primers NONE) to ensure workflow completion
deps: pin package versions in child conda environments chore: cleanup redudant print statements
…s of primer inputs
…shut down unexpectedly (i.e. sigterm or power loss)
…ctory as this is no longer necessary
… scripts for environment/container support
…versions in setup.py
…an integer sampleID
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