skylab

Secondary analysis pipelines for the Human Cell Atlas.

Pipelines

• Smart-seq2 secondary analysis pipeline

Bold indicates that this pipeline is blessed

How to run pipelines from skylab

For now, use git clone git clone git@github.com:HumanCellAtlas/skylab.git and run the pipeline in cromwell.

1. WDL and Cromwell Documentation
2. Running WDLs in Cromwell

[TODO] Update this section with better instructions on how to easily try our pipelines.

[TODO] Blessed HCA Pipelines in Methods Repositories

• Agora
• Dockstore

[TODO] Tagged releases

Pipelines are released in tagged releases to track changes in version of pipeline, and to track when a pipeline is blessed.

[TODO] Automated testing options

[TODO] Onboarding pipelines