Note: All releases may introduce breaking changes until the release of v1.0.0

Documentation

Can be found at https://socialgene.github.io

Usage

:::note If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data. :::

Note that this pipeline can initiate significant number of compute processes. If you are running on a cloud service you alone are responsible for any costs.

outdir="path_to_my/outdir"
outdir_download_cache="path_to_my/outdir_download_cache"

nextflow run  socialgene/sgnf \
  -profile ultraquickstart,docker \
  --outdir $outdir \
  --outdir_download_cache $outdir_download_cache

Unlike nf-core hosted pipelines, you should be able to use configuration files to run the pipeline. A number of examples are available https://github.com/socialgene/sgnf/tree/main/conf/examples

Credits

socialgene/sgnf was originally written by Chase M. Clark.

If you would like to contribute to this pipeline, please see the contributing guidelines.

Contributions and Support

Chase M. Clark (and thus this project) was supported by an NLM training grant to the Computation and Informatics in Biology and Medicine Training Program (NLM 5T15LM007359)

Citations

An extensive list of references for the tools used by the pipeline can be found in the 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.