Introduction

nf-stem is a minimal nf-core pipeline containing as few components as possible. The idea is to be as light as possible while maintaining compatibility with nf-core tools such as modules and subworkflows. You could use this as a template to start your own pipeline or explore alternative methods of working with the nf-core template. It is inspired by kenibrewer/simplenextflow but it has the following differences:

• It is generated using the template and should be compatible with nf-core sync for the foreseeable future
• It uses the nf-validate plugin to reduce boilerplate code
• It removes some additional files such as docs/
• It uses Nextflow code to replace the Java classes in lib/ (see the initialise subworkflow)
• It uses results as a default value for --outdir to remove one additional parameter user need to supply
• It removes email and slack integration for simplicity
• It removes Github features so developers can add their own

You probably shouldn't use this, it's a good POC for how simple nf-core could be in future. If you think you can simplify it, open a PR!

Potential simplifications:

• Remove, move or reduce editor files to make the repo look less messy
• Combine documentation into fewer files to reduce documentation overhead
• Simplify the contents of the Nextflow code itself

I have adapted Ken Brewer's instructions for cloning his template below but updated them for this repo:

Template instructions:

Make your own repo

• [ ] Fork the repo to your own organisation and change the name to something appropriate

Template Naming

• [ ] Replace all instances of nf-stem with the name of your pipeline
• [ ] Replace all instances of adamrtalbot with your GitHub username/organization

Samplesheet handling

• [ ] Update the assets/schema_input.json for your own samplesheet. Use the nf-validate documentation to guide you.

Add needed modules/processes

• [ ] Add any needed nf-core modules via the cli command nf-core modules install
• [ ] Add any custom processes to the modules/local directory
• [ ] Add and required software to the environment.yml file to be installed via conda or wave containers

Modify the main workflow

• [ ] Modify the main.nf file to add any needed processes

Documentation

• [ ] Search for TODO and replace with your own content
• [ ] Delete this section of the README

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.

First, prepare a samplesheet with your input data that looks as follows:

samplesheet.csv:

csv sample,fastq_1,fastq_2 CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz

Now, you can run the pipeline using:

bash nextflow run adamrtalbot/nf-stem \ -profile <docker/singularity/.../institute> \ --input samplesheet.csv

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

adamrtalbot/nf-stem was originally written by Adam Talbot.

We thank the following people for their extensive assistance in the development of this pipeline:

• Ken Brewer (@kenibrewer)

Contributions and Support

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

Citations

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

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.