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Updating usage info
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marchoeppner committed Apr 2, 2024
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[Basic execution](#basic-execution)

[Pipeline version](#specifying-pipeline-version)

[Resources](#resources)

## Basic execution
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In this example, both `--reference_base` and the choice of software provisioning are already set in the local configuration `lsh` and don't have to be provided as command line argument.

## Specifying pipeline version

If you are running this pipeline in a production setting, you will want to lock the pipeline to a specific version. This is natively supported through nextflow with the `-r` argument:

```bash
nextflow run marchoeppner/pipeline -profile lsh -r 1.0 <other options here>
```

The `-r` option specifies a github [release tag](https://github.com/marchoeppner/gabi/releases) or branch, so could also point to `main` for the very latest code release. Please note that every major release of this pipeline (1.0, 2.0 etc) comes with a new reference data set, which has the be [installed](installation.md) separately.

## Resources

The following options can be set to control resource usage outside of a site-specific [config](https://github.com/marchoeppner/nf-configs) file.
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