workflows-nextflow
Workflow management with Nextflow and nf-core
Science Score: 41.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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○DOI references
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○Academic publication links
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✓Committers with academic emails
5 of 18 committers (27.8%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (12.7%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
Workflow management with Nextflow and nf-core
Basic Info
- Host: GitHub
- Owner: carpentries-incubator
- License: other
- Language: Nextflow
- Default Branch: main
- Homepage: https://carpentries-incubator.github.io/workflows-nextflow/
- Size: 20.9 MB
Statistics
- Stars: 25
- Watchers: 5
- Forks: 38
- Open Issues: 29
- Releases: 2
Topics
Metadata Files
README.md
This lesson is an introduction to the workflow manager Nextflow, and nf-core, a community effort to collect a curated set of analysis pipelines built using Nextflow.
Nextflow enables scalable and reproducible scientific workflows using software containers such as Docker and Singularity. It allows the adaptation of pipelines written in the most common scripting languages such as R and Python. Nextflow is a Domain Specific Language (DSL) that simplifies the implementation and the deployment of complex parallel and reactive workflows on clouds and clusters.
This lesson also introduces nf-core: a framework that provides a community-driven, peer reviewed platform for the development of best practice analysis pipelines written in Nextflow.
This lesson motivates the use of Nextflow and nf-core as a development tool for building and sharing computational pipelines that facilitate reproducible (data) science workflows.
Contributing
We welcome all contributions to improve the lesson! Maintainers will do their best to help you if you have any questions, concerns, or experience any difficulties along the way.
We'd like to ask you to familiarize yourself with our Contribution Guide and have a look at the [more detailed guidelines][lesson-example] on proper formatting, ways to render the lesson locally, and even how to write new episodes.
Please see the current list of [issues][https://github.com/carpentries-incubator/workflows-nextflow/issues] for ideas for contributing to this
repository. For making your contribution, we use the GitHub flow, which is
nicely explained in the chapter Contributing to a Project in Pro Git
by Scott Chacon.
Look for the tag 
. This indicates that the maintainers will welcome a pull request fixing this issue.
Maintainer(s)
Current maintainers of this lesson are
- Graeme R. Grimes
- Mahesh Binzer-Panchal
Authors
A list of contributors to the lesson can be found in AUTHORS
Citation
To cite this lesson, please consult with CITATION
Useful Incubator links
Owner
- Name: carpentries-incubator
- Login: carpentries-incubator
- Kind: organization
- Repositories: 107
- Profile: https://github.com/carpentries-incubator
Citation (CITATION)
Please cite this lesson as: Graeme R. Grimes, Evan Floden, Paolo Di Tommaso, Phil Ewels and Maxime Garcia Introduction to Workflows with Nextflow and nf-core. https://github.com/carpentries-incubator/workflows-nextflow 2021. The lesson material was adapted with permission from from seqera labs [nextflow-tutorial](https://github.com/seqeralabs/nextflow-tutorial)
GitHub Events
Total
- Watch event: 3
- Issue comment event: 2
- Push event: 9
- Pull request event: 2
- Fork event: 3
Last Year
- Watch event: 3
- Issue comment event: 2
- Push event: 9
- Pull request event: 2
- Fork event: 3
Committers
Last synced: 12 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Graeme Grimes | G****s@G****m | 663 |
| Mahesh Binzer-Panchal | m****l@n****e | 144 |
| Mahesh Binzer-Panchal | m****l@n****e | 38 |
| Graeme Grimes | g****s@i****k | 37 |
| bobturneruk | b****k@g****m | 25 |
| Nurlan Kerimov | 3****f | 17 |
| Erik Fasterius | e****s@o****m | 13 |
| Alison Meynert | a****2@e****k | 10 |
| Toby Hodges | t****s@g****m | 4 |
| VeBeKay1 | 1****1 | 3 |
| Edward Wallace | e****e | 3 |
| Erin McAuley | e****y@g****m | 2 |
| ameynert | a****t@i****k | 2 |
| Chris Fields | c****s@i****u | 1 |
| Kübra Narcı | k****c@g****m | 1 |
| Graeme Greemes | g****2@s****e | 1 |
| Stathis | i****t | 1 |
| Chia Sin Liew | c****w@h****u | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 43
- Total pull requests: 60
- Average time to close issues: over 1 year
- Average time to close pull requests: about 2 months
- Total issue authors: 7
- Total pull request authors: 12
- Average comments per issue: 1.42
- Average comments per pull request: 0.62
- Merged pull requests: 51
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 2
- Average time to close issues: N/A
- Average time to close pull requests: less than a minute
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 1.5
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- ggrimes (39)
- mahesh-panchal (20)
- tomsing1 (6)
- kerimoff (3)
- ewallace (2)
- ameynert (2)
- unugwa (1)
- tobyhodges (1)
- louisegrimble (1)
- tavareshugo (1)
Pull Request Authors
- ggrimes (43)
- mahesh-panchal (20)
- tobyhodges (4)
- carpentries-bot (3)
- ewallace (3)
- emmcauley (2)
- kerimoff (2)
- ameynert (2)
- cschu (2)
- fasterius (1)
- isthisthat (1)
- bobturneruk (1)
- zkamvar (1)
- chiasinL (1)
- cjfields (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- actions/upload-artifact v3 composite
- actions/checkout v3 composite
- carpentries/actions/check-valid-pr main composite
- carpentries/actions/comment-diff main composite
- carpentries/actions/download-workflow-artifact main composite
- carpentries/actions/download-workflow-artifact main composite
- carpentries/actions/remove-branch main composite
- carpentries/actions/check-valid-pr main composite
- carpentries/actions/comment-diff main composite
- actions/checkout v3 composite
- actions/upload-artifact v3 composite
- carpentries/actions/check-valid-pr main composite
- carpentries/actions/setup-lesson-deps main composite
- carpentries/actions/setup-sandpaper main composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite
- actions/checkout v3 composite
- carpentries/actions/setup-lesson-deps main composite
- carpentries/actions/setup-sandpaper main composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite
- actions/checkout v3 composite
- carpentries/actions/check-valid-credentials main composite
- carpentries/actions/update-lockfile main composite
- carpentries/create-pull-request main composite
- r-lib/actions/setup-r v2 composite
- actions/checkout v3 composite
- carpentries/actions/check-valid-credentials main composite
- carpentries/actions/update-workflows main composite
- carpentries/create-pull-request main composite
- fastqc 0.11.*
- multiqc 1.10.*
- nextflow 20.10.0.*
- nf-core
- salmon 1.5.*
- fastqc 0.11.5.*
- multiqc 1.10.*
- salmon 1.5.*