https://github.com/christopher-hakkaart/templateswebinar
Templates webinar
https://github.com/christopher-hakkaart/templateswebinar
Last synced: 3 months ago
JSON representation
Templates webinar
- Host: GitHub
- URL: https://github.com/christopher-hakkaart/templateswebinar
- Owner: christopher-hakkaart
- License: mit
- Created: 2024-02-20T07:33:32.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2024-02-21T17:43:13.000Z (over 1 year ago)
- Last Synced: 2025-01-13T12:46:39.710Z (5 months ago)
- Language: Nextflow
- Size: 166 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE
- Citation: CITATIONS.md
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README
## Introduction
**seqrea/templateswebinar** 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 seqrea/templateswebinar \
-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).
## Credits
seqrea/templateswebinar was originally written by Chris.
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).
## Citations
An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE).
> **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).