Here we outline, how to credit the work of others as it is incorporated into your pipeline. It is important and critical that we acknowledge those who support our work.

In scripts

If the original concept of your script or parts of the code are borrowed, please acknowledge with a comment at the top.

# This script is based on https://github.com/nf-core/rnaseq/blob/master/bin/check_samplesheet.py
or
# This script was originally conceived by @github-username

In nextflow.config

nextflow.config now has space in the "manifest" for a list of "contributors". The list should everyone who contributed one way or the other to the pipeline. There are three levels of "contribution":

  • maintainer
  • author
  • contributor

In README.md

Under Credits in README.md

  • Acknowledge those who wrote the scripts and local modules
  • Acknowledge those who provide concepts and ideas
  • Acknowledge the code reviewers and those who contributed through discussions
  • Acknowledge nf-core and Nextflow Slack community members for answering queries

In CITATIONS.md

List all pipeline tools with links and references.

- [STAR](https://pubmed.ncbi.nlm.nih.gov/23104886/)

  > Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25. PubMed PMID: 23104886; PubMed Central PMCID: PMC3530905.

- [BBMap](https://sourceforge.net/projects/bbmap/)