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docs: Update README.md #59

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Apr 19, 2024
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16 changes: 8 additions & 8 deletions README.md
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Expand Up @@ -9,11 +9,11 @@
This ReadMe is only a brief introduction, please refer to ReadTheDocs for the latest documentation and a more detailed description of the pipeline.

---
![Lint](https://github.com/clinical-genomics-uppsala/marple_rd_wgs/actions/workflows/lint.yaml/badge.svg?branch=main)
![Snakefmt](https://github.com/clinical-genomics-uppsala/marple_rd_wgs/actions/workflows/snakefmt.yaml/badge.svg?branch=main)
![snakemake dry run](https://github.com/clinical-genomics-uppsala/marple_rd_wgs/actions/workflows/snakemake-dry-run.yaml/badge.svg?branch=main)
![integration test](https://github.com/clinical-genomics-uppsala/marple_rd_wgs/actions/workflows/integration1.yaml/badge.svg?branch=main)
![pycodestyle](https://github.com/clinical-genomics-uppsala/marple_rd_wgs/actions/workflows/pycodestyle.yaml/badge.svg?branch=main)
![Lint](https://github.com/clinical-genomics-uppsala/poirot_rd_wgs/actions/workflows/lint.yaml/badge.svg?branch=main)
![Snakefmt](https://github.com/clinical-genomics-uppsala/poirot_rd_wgs/actions/workflows/snakefmt.yaml/badge.svg?branch=main)
![snakemake dry run](https://github.com/clinical-genomics-uppsala/poirot_rd_wgs/actions/workflows/snakemake-dry-run.yaml/badge.svg?branch=main)
![integration test](https://github.com/clinical-genomics-uppsala/poirot_rd_wgs/actions/workflows/integration1.yaml/badge.svg?branch=main)
![pycodestyle](https://github.com/clinical-genomics-uppsala/poirot_rd_wgs/actions/workflows/pycodestyle.yaml/badge.svg?branch=main)

[![License: GPL-3](https://img.shields.io/badge/License-GPL3-yellow.svg)](https://opensource.org/licenses/gpl-3.0.html)

Expand All @@ -29,12 +29,12 @@ $ cd .tests/integration
$ snakemake -n -s ../../workflow/Snakefile --configfiles ../../config/config.yaml config.yaml
```

## :rocket: [Usage](https://marple-rd-tc.readthedocs.io/en/latest/running/)
## :rocket: [Usage](https://poirot-rd-wgs.readthedocs.io/en/latest/running/)

To use this run this pipeline the requirements in `requirements.txt` must be installed. It is most straightforward to install the requirements inside a python virtual environment created with the python [venv module](https://docs.python.org/3/library/venv.html). The `sample.tsv`, `units.tsv`, `resources.yaml`, and `config.yaml` files need to be available in the current directory (or otherwise specified in `config.yaml`). You always need to specify the `config`-file either in the profile yaml file or in the snakemake command. To run the pipeline:

```bash
$ snakemake --profile /path/to/snakemakeprofile --configfile config.yaml -s /path/to/marple_rd_wgs/workflow/Snakefile
$ snakemake --profile /path/to/snakemakeprofile --configfile config.yaml -s /path/to/poirot_rd_wgs/workflow/Snakefile
```
## :judge: Rule Graph
![rule_graph](images/dag.svg)
![rule_graph](images/dag.svg)
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