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Fix minor paper typos
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Fixes a couple of small typos in an otherwise great paper.
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huddlej committed Nov 1, 2024
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Expand Up @@ -51,13 +51,13 @@ snk install \
-t v2.1.1
```

The workflow will then accessible via the `variant-calling` CLI in the terminal (Figure 1). Additionally, the snk command can be used to list and uninstall workflows installed with Snk. The complete documentation for managing workflows can be found at \url{https://snk.wytamma.com/managing_workflows}.
The workflow will then be accessible via the `variant-calling` CLI in the terminal (Figure 1). Additionally, the snk command can be used to list and uninstall workflows installed with Snk. The complete documentation for managing workflows can be found at \url{https://snk.wytamma.com/managing_workflows}.

![The `variant-calling` CLI generated by Snk.](docs/images/variant-calling-cli.png)

The core functionality of Snk is the dynamic creation of CLIs. Internally snk uses the `Snk-CLI` sister package to generate the CLI. By default key values pairs of the Snakemake configfile are mapped to CLI options e.g. `samples: samples.tsv` in the configfile will generate a `--samples` option in the CLI with the default value `samples.tsv` (Figure 2). The CLI generated by snk is highly customisable and can be configured via a snk.yaml file placed in the workflow directory. The snk.yaml file can configure many aspects of CLI including subcommands, ASCII art, help messages, resource files, default values and much more. Complete documentation for the Snk config file can be found at \url{https://snk.wytamma.com/snk_config_file}.

![The the run command of the `variant-calling` CLI dynamically generated from the Snakemake configfile. Several standard options are provided in the Options section e.g. `--dry` (equivalent to Snakemakes `--dry-run`), `--dag` to create a DAG plot of the workflow, and `--cores` witch defaults to all. The Workflow Configuration section contains the options dynamically generated from the configfile. Snk-CLI automatically infers the defaults and types of the options and creates flags for boolean options.](docs/images/variant-calling-cli-run.png)
![The run command of the `variant-calling` CLI dynamically generated from the Snakemake configfile. Several standard options are provided in the Options section e.g. `--dry` (equivalent to Snakemakes `--dry-run`), `--dag` to create a DAG plot of the workflow, and `--cores` witch defaults to all. The Workflow Configuration section contains the options dynamically generated from the configfile. Snk-CLI automatically infers the defaults and types of the options and creates flags for boolean options.](docs/images/variant-calling-cli-run.png)

Developers can also directly use the Snk-CLI package to generate CLIs for their Snakemake workflows. By using the CLI class from Snk-CLI workflow developers can build a fully featured workflow package without having to write a Snakemake wrapper. We provide a guide for using Snk-CLI to build self contained workflow packages at \url{https://snk.wytamma.com/workflow_packages}. The Snk-CLI package is available via PYPI and can be installed using the command `pip install snk-cli`.

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