Usage

The 3t-seq pipeline leverages Pixi to simplify execution and ensure environment consistency.

Running the Pipeline

To execute the pipeline, use the pixi run test command or call snakemake directly via pixi run.

Using Pixi Tasks

We have predefined several tasks to help you manage the pipeline:

• Environment Setup: Initializes Git LFS and pulls large data files needed for integration tests and some analysis steps.

pixi run setup

• Linting (Spell-checking):

Linting checks your configuration files for typos or formatting errors before you run anything, preventing the pipeline from crashing hours later.

pixi run lint remote-references laptop

• Dry-run (Rehearsal): A dry-run tells the pipeline to plan out all the steps and show you exactly what files it would create and what jobs it would run, without actually doing any of the heavy computations.

pixi run dry-run remote-references laptop

• Execution (Run): This launches the actual data processing.

pixi run test remote-references laptop

Advanced Usage

You can pass extra arguments to Snakemake through Pixi:

pixi run snakemake --cores 8 --use-conda --directory .tests/integration

Reports

After the pipeline completes, you can generate a comprehensive HTML report:

pixi run test-report remote-references laptop

This will create a report.zip file which you can extract to view results in your browser.