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Add a section on some other workflow tools #31

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21 changes: 21 additions & 0 deletions _episodes/10-final-notes.md
Original file line number Diff line number Diff line change
Expand Up @@ -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."
Expand Down Expand Up @@ -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 %}