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

Proof of concept rnaseq pipeline
https://github.com/christopher-hakkaart/pocrnaseq

Last synced: 3 months ago
JSON representation

Proof of concept rnaseq pipeline

• Host: GitHub
• URL: https://github.com/christopher-hakkaart/pocrnaseq
• Owner: christopher-hakkaart
• License: mit
• Created: 2023-11-02T09:53:40.000Z (over 1 year ago)
• Default Branch: main
• Last Pushed: 2023-12-06T23:53:08.000Z (over 1 year ago)
• Last Synced: 2025-01-13T12:46:41.205Z (5 months ago)
• Language: Nextflow
• Size: 2.17 MB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • Contributing: .github/CONTRIBUTING.md
  • License: LICENSE
  • Code of conduct: CODE_OF_CONDUCT.md
  • Citation: CITATIONS.md

Awesome Lists containing this project

README

        
# ![nf-core/pocrnaseq](docs/images/nf-core-pocrnaseq_logo_light.png#gh-light-mode-only) ![nf-core/pocrnaseq](docs/images/nf-core-pocrnaseq_logo_dark.png#gh-dark-mode-only)

[![GitHub Actions CI Status](https://github.com/nf-core/pocrnaseq/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/pocrnaseq/actions?query=workflow%3A%22nf-core+CI%22)

[![GitHub Actions Linting Status](https://github.com/nf-core/pocrnaseq/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/pocrnaseq/actions?query=workflow%3A%22nf-core+linting%22)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/pocrnaseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)

[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)

[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)

[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)

[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)

[![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/pocrnaseq)

[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23pocrnaseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/pocrnaseq)[![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/pocrnaseq** 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/pocrnaseq \

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

## Credits

nf-core/pocrnaseq was originally written by Chirs 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 `#pocrnaseq` channel](https://nfcore.slack.com/channels/pocrnaseq) (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).