https://github.com/christopher-hakkaart/nanogenvar
Pipeline for variant calling nanopore data.
https://github.com/christopher-hakkaart/nanogenvar
Last synced: 3 months ago
JSON representation
Pipeline for variant calling nanopore data.
- Host: GitHub
- URL: https://github.com/christopher-hakkaart/nanogenvar
- Owner: christopher-hakkaart
- License: mit
- Created: 2024-03-10T19:51:10.000Z (about 1 year ago)
- Default Branch: main
- Last Pushed: 2024-03-10T19:51:52.000Z (about 1 year ago)
- Last Synced: 2025-01-13T12:46:42.226Z (5 months ago)
- Language: Nextflow
- Size: 321 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
- Citation: CITATIONS.md
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## Introduction
**nf-core/nanogenvar** is a bioinformatics pipeline that ...
1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
## Usage
> [!NOTE]
> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
Now, you can run the pipeline using:
```bash
nextflow run nf-core/nanogenvar \
-profile \
--input samplesheet.csv \
--outdir
```
> [!WARNING]
> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/nanogenvar/usage) and the [parameter documentation](https://nf-co.re/nanogenvar/parameters).
## Pipeline output
To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/nanogenvar/results) tab on the nf-core website pipeline page.
For more details about the output files and reports, please refer to the
[output documentation](https://nf-co.re/nanogenvar/output).
## Credits
nf-core/nanogenvar was originally written by Chris Hakkaart.
We thank the following people for their extensive assistance in the development of this pipeline:
## Contributions and Support
If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).
For further information or help, don't hesitate to get in touch on the [Slack `#nanogenvar` channel](https://nfcore.slack.com/channels/nanogenvar) (you can join with [this invite](https://nf-co.re/join/slack)).
## Citations
An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
You can cite the `nf-core` publication as follows:
> **The nf-core framework for community-curated bioinformatics pipelines.**
>
> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
>
> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).