Comments (4)
ocaisa
commented on July 16, 2024
There's a useful flow chart from CSC to guide you through workflow tools recommendations based on your use case.
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bkmgit
commented on July 16, 2024
Can look at this.
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bkmgit
commented on July 16, 2024
One alternative is the Concise Common Workflow Language which seems to also be used in bioinformatics , an overview is available in this Guix HPC blog post. The CSC guide above seems to indicate that Conda is not great for HPC, and should be packaged. It does recommend GNU parallel for some use cases. @mikerenfro @wirawan0 comments welcome
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bkmgit
commented on July 16, 2024
Related work:
- https://github.com/biosustain/snakemake_UmetaFlow
- https://www.kitware.com/hpccloud-hpc-simulation-workflow-in-the-cloud/
- https://pdc-support.github.io/hpc-intro/12-workflows/
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Related Issues (20)
- Generating our data files
- Locations where we may need to use templates HOT 2
- "Perfect" `snakemake` file for Amdahls Law HOT 1
- Plotting Amdahl's Law HOT 4
- Review lesson objectives HOT 9
- SnakeMake best practices HOT 5
- Location of final code products HOT 2
- Add versions to requirements.txt HOT 5
- Carpentries Workbench
- Moore's law
- Create a profile
- Add description of of `-j` in the compute cluster configuration.
- Inline Python -> Lesson 10
- Flags on Amdahl
- Develop Snakefile on a node
- Consider Parsl HOT 2
- primer docs for sprinters HOT 1
- spelling & linting actions HOT 1
- protect default branch before sprint HOT 1
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