https://github.com/christopher-hakkaart/mypipeline3

This doesn't matter today
https://github.com/christopher-hakkaart/mypipeline3

Last synced: 3 months ago
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This doesn't matter today

• Host: GitHub
• URL: https://github.com/christopher-hakkaart/mypipeline3
• Owner: christopher-hakkaart
• License: mit
• Created: 2024-05-22T18:41:52.000Z (about 1 year ago)
• Default Branch: TEMPLATE
• Last Pushed: 2024-05-22T20:26:53.000Z (about 1 year ago)
• Last Synced: 2025-01-13T12:46:42.230Z (5 months ago)
• Language: Nextflow
• Size: 298 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 2
• 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/myfirstpipeline** 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/myfirstpipeline \

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

## Credits

nf-core/myfirstpipeline 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).

For further information or help, don't hesitate to get in touch on the [Slack `#myfirstpipeline` channel](https://nfcore.slack.com/channels/myfirstpipeline) (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).