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ljwharbers merged 2 commits into from
Dec 1, 2025
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Update Zenodo DOI in README.md #110

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Update Zenodo DOI in README.md
robert-a-forsyth Dec 1, 2025
8d31c06
add metromap
robert-a-forsyth Dec 1, 2025
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7 changes: 4 additions & 3 deletions README.md
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
# IntGenomicsLab/lrsomatic

[![GitHub Actions CI Status](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/nf-test.yml/badge.svg)](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/nf-test.yml)
[![GitHub Actions Linting Status](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/linting.yml/badge.svg)](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
[![GitHub Actions Linting Status](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/linting.yml/badge.svg)](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.17751829-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.17751829)
[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)

[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
Expand All @@ -23,6 +23,8 @@ Developed using **Nextflow DSL2**, it offers high portability and scalability ac

## Pipeline summary

![image](./assets/lrsomatic_1.0.png)

**1) Pre-processing:**

a. Raw read QC ([`cramino`](https://github.com/wdecoster/cramino))
Expand Down Expand Up @@ -159,8 +161,7 @@ If you would like to contribute to this pipeline, please see the [contributing g

## Citations

<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
<!-- If you use IntGenomicsLab/lrsomatic for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
If you use IntGenomicsLab/lrsomatic for your analysis, please cite it using the following doi: [10.5281/zenodo.17751829](https://doi.org/10.5281/zenodo.17751829)

An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.

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