We have some biomedical raw data that need to be preprocessing before uploading to gen3. The preprocessing has multiple steps, so we want to get it done automated. Are there any Linux-based workflow management tools that can be used and connect to Gen3? Thank you very much.
apologies for the late response.
we are currently developing a workflow management tool within Gen3 but it's not ready, yet. Thus, we recommend using external tools (e.g. SnakeMake, Nextflow, CWL/WDL + Cromwell or within Terra or Seven Bridges Cavatica) for data processing and then automating the data ingestion to Gen3 using the APIs (more information here).
Thank you very much for your reply! It helps a lot! For those external tools, which one you think Gen3 supports the best? We will start from scratch, so we want to choose the one with longer support. Thank you again.
At this time, it would not make any difference as to which tool you would use because you can submit data to Gen3 once you have the data processed with any tool best of luck!
Thank you very much!