NBIS-support-framework

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NBIS-support-framework

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A framework for support projects, including templates for reports, data management as well as links to tools and pipelines

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# NBIS Support Framework

## Introduction

The NBIS Support Framework (NBIS-SF) is about creating a collaborative framework
for NBIS support projects and the related data management plans. The idea is to
have a common framework and knowledge-base that NBIS experts may choose to adopt
and expand as they perform support-related work. This includes tools for
reproducibility (_e.g._ Conda, Snakemake, Docker), version control (git,
GitHub), information required to be in NBIS reports and [report
templates](doc/report/) (_e.g._ RMarkdown, LaTeX, KnitR, Jupyter), as well as
support-related information ([data management guidelines](doc/data-management/),
consultation guidelines, contract templates, _etc._). NBIS also has a separate
repository for pipelines, which you can find at
[NBISweden/pipelines][nbis-pipelines]. For more information regarding working
reproducibly in NBIS, please check out the NBIS course [Tools for Reproducible
Research](https://nbisweden.github.io/workshop-reproducible-research/).

You can find more complete examples and inspiration of how to work reproducibly
in NBIS support work at the following places:

- [Mahesh's NBIS project template](https://github.com/mahesh-panchal/NBIS_project_template)
- [Erik's NBIS project template](https://github.com/fasterius/nbis-support-template)
- [Roy's R Markdown templates](https://github.com/royfrancis/minty)
- [Erik's NBIS Quarto template](https://github.com/NBISweden/nbis-templates-quarto)
- [NBIS Assembly project template](https://github.com/NBISweden/assembly-project-template)
- [Rasmus' project template](https://github.com/NBISweden/project_template)
- [Cormac's peer review track project template](https://github.com/NBISweden/CMK-NBIS-PRT-project-template)
- [Cookiecutter Data Science](http://drivendata.github.io/cookiecutter-data-science/)

## Setup

First create a new repository for your project by using NBIS-SF as a template.
You can do this directly from the NBIS-SF GitHub by pressing the _"Use this
template"_ button and select _"Create new repository"_. This will take you through
the creation of your new repo like normal, but it will contain all the content currently
available on NBIS-SF in a single, initial commit. Set the _Owner_ to
[NBISweden](https://github.com/NBISweden/).

### Naming the repository

- For _user-fee projects_, name your new repository with _NBIS_, the Redmine
  issue number, the year, plus a descriptive name, _e.g._ _NBIS-4412-18-mast_.
  You can then clone your new repository like you would normally.

- For _peer-review projects_, name your new repository with _NBIS_ followed by
  the WABI ID of the project. The WABI ID is comprised of the PI's first name
  initial(s), the PI's surname, and the year and month (YYMM) of the application
  deadline. For example: _NBIS-M_Bergö_1305_

> **Note** <br>
> If you don't know the WABI ID for the project, you can ask your manager or
> search for the project in Redmine. The Redmine issue for the project should
> have a field "WABI ID" containing the ID.

## Repo privacy settings

By default repositories are public, meaning they are accessible to anyone on the
Internet. In case, you want to restrict access to the repo to inside NBIS only:

- While creating repo choose "Private"
- Go to repository "Settings" -> "Collaborators and Teams" -> search field in
  "Manage Access" and type "Staff"
- Give appropriate access to "Staff" team (Read, Write, Triage etc.) and voilá,
  now all at NBIS have access

## Contributing

All contributions are welcome, small and large! The central idea behind NBIS-SF
is to develop an up-to-date framework for NBIS support projects, to share
knowledge and to streamline common bioinformatics tasks. Anybody working at
NBIS is welcome to contribute! If you want to contribute something, please see
the [CONTRIBUTING.md](CONTRIBUTING.md) file.

Questions and feedback can be sent to
[Erik Fasterius](mailto:erik.fasterius@nbis.se?subject=[NBIS-SF]),
[Olga Dethlefsen](mailto:olga.dethlefsen@nbis.se?subject=[NBIS-SF]) or
[John Sundh](mailto:john.sundh@nbis.se?subject=[NBIS-SF]).

[nbisweden]: https://github.com/NBISweden
[nbis-pipelines]: https://github.com/NBISweden/pipelines/

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