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teemukataja committed Jun 29, 2023
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7 changes: 5 additions & 2 deletions docs/computing/running/throughput.md
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E -->|Serial| F(<a href='/support/tutorials/many/'>GNU Parallel</a><br><a href='/computing/running/array-jobs/'>Array jobs</a><br><a href='/apps/hyperqueue/'>HyperQueue</a>)
E -->|Parallel| G(Single- or multinode subtasks?)
G -->|Single| H(Dependencies between subtasks?)
G -->|Multi| I(<a href='/computing/running/fireworks/'>FireWorks</a>)
H -->|Yes| J(<a href='https://snakemake.readthedocs.io/en/stable/'>Snakemake</a><br><a href='/support/tutorials/nextflow-puhti/'>Nextflow</a><br><a href='/computing/running/fireworks/'>FireWorks</a>)
G -->|Multi| I(<a href='/computing/running/fireworks/'>FireWorks</a><br><a href='/computing/running/toil-cwl-runner/'>Toil-CWL-Runner</a>)
H -->|Yes| J(<a href='https://snakemake.readthedocs.io/en/stable/'>Snakemake</a><br><a href='/support/tutorials/nextflow-puhti/'>Nextflow</a><br><a href='/computing/running/fireworks/'>FireWorks</a><br><a href='/computing/running/toil-cwl-runner/'>Toil-CWL-Runner</a>)
H -->|No| K(<a href='/apps/hyperqueue/'>HyperQueue</a>)
```

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with `xargs`, see [xargsjob.sh] for example.
* [FireWorks] is a flexible tool for defining, managing and
executing workflows with multiple steps and complex dependencies
* [Toil-CWL-Runner] is an open source workflow manager using the Common
Workflow Language open standards
* [HyperQueue] is a tool for efficient sub-node task scheduling
* [Nextflow workflows using HyperQueue as an executor] can be leveraged to run
large workflows involving thousands of processes efficiently
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[HyperQueue]: ../../apps/hyperqueue.md
[GNU Parallel]: ../../support/tutorials/many.md
[FireWorks]: fireworks.md
[Toil-CWL-Runner]: toil-cwl-runner.md
[contact CSC Service Desk]: ../../support/contact.md
[Nextflow]: ../../support/tutorials/nextflow-puhti.md
[Snakemake]: https://snakemake.readthedocs.io/en/stable/
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1 change: 1 addition & 0 deletions docs/support/tutorials/index.md
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* [General high-throughput guidelines](../../computing/running/throughput.md)
* [Running Nextflow workflows using HyperQueue](nextflow-hq.md)
* [FireWorks workflow manager](../../computing/running/fireworks.md)
* [Toil CWL workflow manager](../../computing/running/toil-cwl-runner.md)
* [How to run many short jobs with GNU Parallel](many.md)
* [HyperQueue meta-scheduler](../../apps/hyperqueue.md)

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