Introduction

nf-core/plumb is a pipeline that generates a publicly accessible database that integrates structural and thermodynamic data for diverse protein-ligand systems, prioritizing reproducibility. The database will be built from known protein-ligand complexes and include docked congeneric ligand series to represent a broad chemical space, with quality control processes to evaluate the quality of docked poses. This effort is conducted in conjunction with the Living Journal of Computational Molecular Sciences paper, “Best Practices for Constructing, Preparing, and Evaluating Protein-Ligand Binding Affinity Benchmarks [Article v1.0],” which aims to create a fully self-consistent, open community resource and set of best practices free from any particular commercial vendor influence.

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.

Now, you can run the pipeline using:

bash nextflow run nf-core/plumb \ -profile <docker/singularity/.../institute> \ --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.

For more details and further functionality, please refer to the usage documentation and the parameter documentation.

Pipeline output

To see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation.

Credits

nf-core/plumb was originally written by Ariana Brenner Clerkin.

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.

For further information or help, don't hesitate to get in touch on the Slack #plumb channel (you can join with this invite).

Citations

<!-- If you use nf-core/plumb for your analysis, please cite it using the following doi: 10.5281/zenodo.XXXXXX --><!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->

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.