diff --git a/_episodes/10-final-notes.md b/_episodes/10-final-notes.md index fcee182..493c575 100644 --- a/_episodes/10-final-notes.md +++ b/_episodes/10-final-notes.md @@ -8,6 +8,7 @@ objectives: - "Understand how to perform a dry-run of your workflow." - "Understand how to configure logging so that each rule generates a separate log." - "Understand how to visualise your workflow." +- "Other workflow tools." keypoints: - "`snakemake -n` performs a dry-run." - "Using log files can make your workflow easier to debug." @@ -180,4 +181,24 @@ Note that this requires the installation of additional Python packages. The Snakemake documentation is located at [snakemake.readthedocs.io](http://snakemake.readthedocs.io) +## Other Workflow Tools + +Snakemake is not the only tool available for managing your worklfows. Many +of the concepts you have learned and practised are applicable to other tools. +Some other tools that might be of interest are: +- [Nextflow](https://www.nextflow.io/): A Python based tool often used in +genomics +- [GNU Parallel](https://www.gnu.org/software/parallel/): A light tool that +extends the BASH shell to run multiple tasks at once +- [Balsam](https://balsam.readthedocs.io/en/latest/): A Python tool to enable +submitting and managing jobs, in particular on supercomputers +- [Fireworks](https://materialsproject.github.io/fireworks/): A Python tool +used by the materials science community to manage workflows on supercomputers +- [Parsl](https://parsl-project.org/): A parallel Python scripting library +- [The Concise Common Workflow Language (CCWL](https://ccwl.systemreboot.net/): +A workflow tool embedded in Guile scheme lisp dialect +- [Guix Workflow Language (GWL)](https://guixwl.org/): A workflow tool using +the Guile scheme and a Python like extension to Guile scheme that enables +running jobs on supercomputers + {% include links.md %}