plumber-pants is a base template and framework to build Nextflow pipelines.
If you're already invested in the nf-core ecosystem or looking to fork an existing nf-core pipelines, I highly recommend checking out the amazing nf-core tools package instead of plumber-pants. However, if you are looking for a more trimmed back framework to start from, without a lot of the unnecessary files for building institution specific pipelines, then plumber-pants might be a helpful resource.
It's nothing fancy just a nice clean starting point to work from when making a new pipeline, allowing you in integrate a lot of your own internal modules. Shoutout if you have any suggestions or want to help improve this template.
If you are using plumber-pants as the base framework for your new pipeline chances are your don't want or need the git history associated with this repo. To download the latest commits without history run:
git clone git@github.com:lpembleton/plumber-pants.git --depth 1
To remove the association with git before you make your own repo:
rm .git
To set up your pipeline, simply delete this README file and replace it with your own documentation. This will allow you to provide clear instructions, explanations, and details specific to your pipeline.
The folder structure is reasonably self-explanatory:
- conf - store your profile specific config files here (
more info) - docs - add any pipeline specific documentation or example data here
- modules - save your modules here (more info below) (
more info) - workflow - you might just have a single pipeline or multiple. Store them here and reference them from the main.nf file in the base dir (`more info)
You can run our own module repository and share these across your pipelines using git submodules
To setup your own module repository:
- Create a GitHub repository such as 'nf-modules'
- I would also recommend creating a subfolder 'local' so that you can still bring in nf-core modules into another subfolder 'nf-core'
- Start adding your internal modules
To link your module repository to your pipeline:
-
Firstly you need to remove the current
modulesfolder in plumber-pantsrm -r modules -
Add your global modules repository as a submodule
git submodule add https://github.com/<user>/<nf-modules> modules -
If you are running an older version git you may need to run the following to pull down the files
git submodule update --init --recursive -
Over time to pull in any updates from your modules repository run:
git submodule update --recursive
Note: you can edit modules within your new pipeline and commit them back to your global module repo. Read this github blog post for some points on how to get started with that.
Contributions to plumber-pants are welcome and encouraged. If you have any ideas, suggestions, or improvements, please feel free to contribute and help enhance this template.
plumber-pants was originally written by LWPembleton.
A lot of inspiration and structure was taken from the Nextflow documentation, the fantastic nf-core community and tool package.
Nextflow enables reproducible computational workflows.
Paolo Di Tommaso, Maria Chatzou, Evan Floden, Pablo Prieto Barja, Emilio Palumbo & Cedric Notredame.
P. Di Tommaso, et al. Nextflow enables reproducible computational workflows. Nature Biotechnology 35, 316–319 (2017) doi:10.1038/nbt.3820
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.
Groovy functions that parse a samplesheet for metadata were sourced from the nf-core (sarek) pipeline
Garcia M, Juhos S, Larsson M et al.
Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants [version 2; peer review: 2 approved]
F1000Research 2020, 9:63 doi: 10.12688/f1000research.16665.2.
This project is licensed under the MIT License - see the LICENSE file for details.