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https://github.com/stephenturner/nf-core-mypipeline

Last synced: 6 days ago
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Host: GitHub
URL: https://github.com/stephenturner/nf-core-mypipeline
Owner: stephenturner
License: mit
Created: 2024-09-09T09:30:55.000Z (about 2 months ago)
Default Branch: main
Last Pushed: 2024-09-09T13:42:22.000Z (about 2 months ago)
Last Synced: 2024-09-09T16:35:22.009Z (about 2 months ago)
Language: Nextflow
Size: 330 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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[![GitHub Actions CI Status](https://github.com/nf-core/mypipeline/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/mypipeline/actions/workflows/ci.yml)

[![GitHub Actions Linting Status](https://github.com/nf-core/mypipeline/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/mypipeline/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/mypipeline/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)

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[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/mypipeline)

[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23mypipeline-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/mypipeline)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)

## Introduction

**nf-core/mypipeline** 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/mypipeline \

   -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/mypipeline/usage) and the [parameter documentation](https://nf-co.re/mypipeline/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/mypipeline/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/mypipeline/output).

## Credits

nf-core/mypipeline was originally written by Stephen D. Turner.

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 `#mypipeline` channel](https://nfcore.slack.com/channels/mypipeline) (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).