OpenScPCA-nf

A workflow for running analysis modules ported from the OpenScPCA-analysis repository to Nextflow.

See https://github.com/AlexsLemonade/OpenScPCA-admin/blob/main/technical-docs/nextflow-workflow-specifications.md for initial implementation plans for this workflow.

Running the workflow

The workflow is currently set up to run best via AWS batch, but some testing may work locally. You will need to have appropriate AWS credentials set up to run the workflow on AWS and access the data files.

Running the workflow manually

Alternatively, you can run the workflow locally. The following base command will run the main workflow, assuming all AWS permissions are set up correctly:

nextflow run AlexsLemonade/OpenScPCA-nf -profile batch

For many use cases you may want to use the --results_bucket argument to avoid writing to the default output bucket (the default is a staging bucket, but may not be accessible to all users). Note that despite the name, this can be a local directory as well as an S3 bucket. For an S3 bucket, the format should be s3://bucket-name/path/to/results.

nextflow run AlexsLemonade/OpenScPCA-nf -profile batch --results_bucket {OUTDIR}

Profiles

To run the workflow with simulated data, you can add the simulated profile. As with the main workflow, you will want to specify an output directory for the simulated results with the --results_bucket argument.

nextflow run AlexsLemonade/OpenScPCA-nf -profile batch,simulated --results_bucket {SIM_RESULTS_DIR}

Entry points

The workflow also has a couple of entry points other than the main workflow, for testing and creating simulated data.

To run a test version of the workflow to check permissions and infrastructure setup:

nextflow run AlexsLemonade/OpenScPCA-nf -profile batch -entry test

To run the workflow that creates simulated SCE objects for the OpenScPCA project, you can use the following command, which specifies running the workflow with the simulate entry point. Note that you will need to specify the directory for the simulation output using the --sim_pubdir argument, as the default output bucket is not writeable except by a few specific roles:

nextflow run AlexsLemonade/OpenScPCA-nf -profile batch -entry simulate --sim_pubdir {SIMDIR}

Stub runs

All of the above commands will run the complete workflow processes. To test the general logic of the workflow without running the full workflow you can use a stub run by including the -stub argument and -profile stub.

nextflow run AlexsLemonade/OpenScPCA-nf -stub -profile stub

This version of the workflow is run for every pull request to the main branch.

Repository setup

This repository uses pre-commit to enforce code style and formatting. To install the pre-commit hooks described in .pre-commit-config.yaml, run the following command in the repository root:

pre-commit install

Workflow releases

This repository employs two different release strategies; one for tracking the workflow code itself, and one used to track the underlying data being used for workflow runs.

Code releases

When the code of the workflow changes significantly, we use GitHub releases to create a tag using semantic versioning (e.g. v1.0.0). The creation of a release on GitHub will trigger a workflow run using the current data release, as specified in nextflow.config by the release_prefix parameter. This run will replace the data in the results bucket for the current data release with the updated results from the workflow run.

Data releases

When a new OpenScPCA data release is created, the release_prefix parameter will be updated, and a Git tag will be added with the format YYYY-MM-DD (e.g. 2024-07-08), matching the value of release_prefix. This will trigger a workflow run for the purposes of populating the results bucket, but these tags should not be used as releases on GitHub.