otuseq

Pipeline created for a client that still use OTUs and do not want to move to ASVs. :(

Introduction

::: warning This is a warning :::

leleonp/template is a bioinformatics pipeline that ...

Usage

Note

If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow.

Now, you can run the pipeline using:

nextflow run main.nf \
   -profile docker  \
   --input samplesheet.csv \
   --outdir <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.

Credits

leleonp/template was originally written by Luis E. Leon.

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.

Citations

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT 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.