# qcif/taxodactyl

# qcif/taxodactyl [![GitHub Actions CI Status](https://github.com/qcif/taxodactyl/actions/workflows/ci.yml/badge.svg)](https://github.com/qcif/taxodactyl/actions/workflows/ci.yml) [![GitHub Actions Linting Status](https://github.com/qcif/taxodactyl/actions/workflows/linting.yml/badge.svg)](https://github.com/qcif/taxodactyl/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.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 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/qcif/taxodactyl) ## Introduction **qcif/taxodactyl** is a bioinformatics pipeline that ... ## 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 qcif/taxodactyl \ -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/docs/usage/getting_started/configuration#custom-configuration-files). ## Credits qcif/taxodactyl was originally written by Magdalena Antczak, Cameron Hyde, Daisy Li. 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/main/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).

License
  MIT

## Contents

- ["qcif/taxodactyl"]
- assets/
- conf/
- workflows/
- subworkflows/
- nextflow.config
- README.md
- nextflow_schema.json
- LICENSE
- CITATIONS.md
- modules.json
- .nf-core.yml
- .pre-commit-config.yaml
- .prettierignore