io.nextflow:nextflow
A DSL for data-driven computational pipelines
Science Score: 77.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 2 DOI reference(s) in README -
✓Academic publication links
Links to: nature.com, acm.org -
✓Committers with academic emails
15 of 212 committers (7.1%) from academic institutions -
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (15.1%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
A DSL for data-driven computational pipelines
Basic Info
- Host: GitHub
- Owner: nextflow-io
- License: apache-2.0
- Language: Groovy
- Default Branch: master
- Homepage: http://nextflow.io
- Size: 60.8 MB
Statistics
- Stars: 3,128
- Watchers: 87
- Forks: 723
- Open Issues: 487
- Releases: 302
Topics
Metadata Files
README.md
"Dataflow variables are spectacularly expressive in concurrent programming"
Henri E. Bal , Jennifer G. Steiner , Andrew S. Tanenbaum
Nextflow is a workflow system for creating scalable, portable, and reproducible workflows. It is based on the dataflow programming model, which greatly simplifies the writing of parallel and distributed pipelines, allowing you to focus on the flow of data and computation. Nextflow can deploy workflows on a variety of execution platforms, including your local machine, HPC schedulers, AWS Batch, Azure Batch, Google Cloud Batch, and Kubernetes. Additionally, it supports many ways to manage your software dependencies, including Conda, Spack, Docker, Podman, Singularity, and more.
Quick start
Install Nextflow with a single command:
bash
curl -fsSL https://get.nextflow.io | bash
It creates the nextflow executable file in the current directory. You can then move it to a directory in your $PATH to run it from anywhere.
Nextflow can also be installed from Bioconda:
bash
conda install -c bioconda nextflow
Documentation
The Nextflow documentation is available for the latest stable and edge releases.
Community
You can post questions and get help in the Nextflow community forum or the Nextflow Slack. Bugs and feature requests should be reported as GitHub issues.
The Nextflow community is highly active with regular community meetings, events, a podcast and more. You can view much of this material on the Nextflow and nf-core YouTube channels.
The nf-core project is a community effort aggregating high quality Nextflow workflows which can be used by everyone.
Contributing
Contributions are more than welcome. See the CONTRIBUTING file for details.
License
Nextflow is released under the Apache 2.0 license. Nextflow is a registered trademark.
Citations
If you use Nextflow in your work, please cite:
P. Di Tommaso, et al. Nextflow enables reproducible computational workflows. Nature Biotechnology 35, 316319 (2017) doi:10.1038/nbt.3820
Credits
Nextflow is built on two *great* open-source software projects, Groovy and GPars.
YourKit is kindly supporting Nextflow with its fully-featured Java Profiler.
Owner
- Name: nextflow-io
- Login: nextflow-io
- Kind: organization
- Website: http://nextflow.io
- Repositories: 78
- Profile: https://github.com/nextflow-io
Citation (CITATION.cff)
cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Di Tommaso"
given-names: "Paolo"
orcid: "https://orcid.org/0000-0003-3220-0253"
- family-names: "Chatzou"
given-names: "Maria"
- family-names: "Floden"
given-names: "Evan"
orcid: "https://orcid.org/0000-0002-5431-190X"
- family-names: "Prieto Barja"
given-names: "Pablo"
- family-names: "Palumbo"
given-names: "Emilio"
orcid: "https://orcid.org/0000-0003-4599-8161"
- family-names: "Notredame"
given-names: "Cedric"
orcid: "https://orcid.org/0000-0003-1461-0988"
title: "Nextflow enables reproducible computational workflows"
version: 1.0.0
doi: 10.1038/nbt.3820
date-released: 2017-04-11
url: "https://nextflow.io"
GitHub Events
Total
- Fork event: 95
- Create event: 343
- Commit comment event: 5
- Release event: 22
- Issues event: 593
- Watch event: 327
- Delete event: 292
- Member event: 4
- Issue comment event: 2,915
- Push event: 1,596
- Pull request event: 848
- Pull request review event: 1,493
- Pull request review comment event: 1,299
Last Year
- Fork event: 95
- Create event: 343
- Commit comment event: 5
- Release event: 22
- Issues event: 594
- Watch event: 328
- Delete event: 292
- Member event: 4
- Issue comment event: 2,916
- Push event: 1,596
- Pull request event: 848
- Pull request review event: 1,493
- Pull request review comment event: 1,299
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Paolo Di Tommaso | p****o@g****m | 5,870 |
| Ben Sherman | b****n@g****m | 359 |
| Phil Ewels | p****s@s****o | 77 |
| Jorge Ejarque | j****e | 51 |
| Jorge Aguilera | 9****a | 44 |
| Marcel Ribeiro Dantas | m****s@s****o | 39 |
| Adam Talbot | 1****t | 36 |
| Chris Hakkaart | c****t@s****o | 31 |
| Dr Marco Claudio De La Pierre | m****e@g****m | 25 |
| Manuele Simi | m****2@m****u | 25 |
| Abhinav Sharma | a****v | 24 |
| Robert Syme | r****e@g****m | 21 |
| Fabian Lehmann | 4****n | 19 |
| bmsanjuan | b****n@g****m | 17 |
| Jordi Deu-Pons | j****i@j****t | 16 |
| Emilio Palumbo | e****o@g****m | 16 |
| Kevin Sayers | K****s | 13 |
| Tom Sellman | t****n@s****o | 12 |
| Llewellyn vd Berg | 1****l | 12 |
| Evan Floden | e****n@g****m | 11 |
| Michael Smoot | m****t@s****m | 9 |
| xhejtman | x****n@g****m | 7 |
| bmsanjuan | b****Â@g****m | 6 |
| Jose Espinosa-Carrasco | k****u@g****m | 6 |
| Paul Madden | m****p@c****u | 5 |
| Nathan Johnson | s****n | 5 |
| Mike Smoot | m****s@a****m | 5 |
| Josh Chorlton | j****l | 5 |
| Jonathan Manning | j****g@e****k | 5 |
| Patrick Hüther | p****r@g****m | 5 |
| and 182 more... | ||
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 978
- Total pull requests: 1,332
- Average time to close issues: 8 months
- Average time to close pull requests: about 1 month
- Total issue authors: 495
- Total pull request authors: 127
- Average comments per issue: 3.18
- Average comments per pull request: 3.34
- Merged pull requests: 747
- Bot issues: 0
- Bot pull requests: 4
Past Year
- Issues: 394
- Pull requests: 919
- Average time to close issues: 15 days
- Average time to close pull requests: 9 days
- Issue authors: 227
- Pull request authors: 74
- Average comments per issue: 1.09
- Average comments per pull request: 2.67
- Merged pull requests: 556
- Bot issues: 0
- Bot pull requests: 3
Top Authors
Issue Authors
- bentsherman (45)
- adamrtalbot (41)
- ewels (39)
- pditommaso (39)
- nick-youngblut (23)
- stevekm (20)
- robsyme (20)
- VasLem (13)
- mahesh-panchal (13)
- bskubi (9)
- siddharthab (9)
- Puumanamana (9)
- marcodelapierre (9)
- nvnieuwk (7)
- gdevenyi (7)
Pull Request Authors
- bentsherman (408)
- pditommaso (228)
- jorgee (131)
- adamrtalbot (82)
- ewels (63)
- christopher-hakkaart (61)
- tom-seqera (32)
- marcodelapierre (27)
- robsyme (16)
- Lehmann-Fabian (14)
- edmundmiller (11)
- nschan (10)
- alberto-miranda (10)
- rcannood (10)
- siddharthab (8)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 19
- Total downloads: unknown
-
Total dependent packages: 33
(may contain duplicates) -
Total dependent repositories: 19
(may contain duplicates) - Total versions: 1,662
proxy.golang.org: github.com/nextflow-io/nextflow
- Documentation: https://pkg.go.dev/github.com/nextflow-io/nextflow#section-documentation
- License: apache-2.0
-
Latest release: v24.10.9+incompatible
published 8 months ago
Rankings
repo1.maven.org: io.nextflow:nextflow
A DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner
- Homepage: http://www.nextflow.io
- Documentation: https://appdoc.app/artifact/io.nextflow/nextflow/
- License: The Apache License, Version 2.0
-
Latest release: 24.10.8
published 9 months ago
Rankings
repo1.maven.org: io.nextflow:nf-commons
A DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner
- Homepage: http://www.nextflow.io
- Documentation: https://appdoc.app/artifact/io.nextflow/nf-commons/
- License: The Apache License, Version 2.0
-
Latest release: 24.10.8
published 9 months ago
Rankings
repo1.maven.org: io.nextflow:nf-amazon
A DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner
- Homepage: http://www.nextflow.io
- Documentation: https://appdoc.app/artifact/io.nextflow/nf-amazon/
- License: Apache 2.0
-
Latest release: 20.10.0
published over 5 years ago
Rankings
repo1.maven.org: io.nextflow:nf-google
A DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner
- Homepage: http://www.nextflow.io
- Documentation: https://appdoc.app/artifact/io.nextflow/nf-google/
- License: Apache 2.0
-
Latest release: 20.10.0
published over 5 years ago
Rankings
repo1.maven.org: io.nextflow:nf-httpfs
A DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner
- Homepage: http://www.nextflow.io
- Documentation: https://appdoc.app/artifact/io.nextflow/nf-httpfs/
- License: The Apache License, Version 2.0
-
Latest release: 24.10.8
published 9 months ago
Rankings
repo1.maven.org: io.nextflow:nf-ga4gh
A DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner
- Homepage: http://www.nextflow.io
- Documentation: https://appdoc.app/artifact/io.nextflow/nf-ga4gh/
- License: Apache 2.0
-
Latest release: 20.10.0
published over 5 years ago
Rankings
repo1.maven.org: io.nextflow:nf-ignite
A DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner
- Homepage: http://www.nextflow.io
- Documentation: https://appdoc.app/artifact/io.nextflow/nf-ignite/
- License: Apache 2.0
-
Latest release: 19.10.0
published over 6 years ago
Rankings
repo1.maven.org: io.nextflow:nf-console
A DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner
- Homepage: http://www.nextflow.io
- Documentation: https://appdoc.app/artifact/io.nextflow/nf-console/
- License: Apache 2.0
-
Latest release: 20.10.0
published over 5 years ago
Rankings
repo1.maven.org: io.nextflow:nf-tower
A DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner
- Homepage: http://www.nextflow.io
- Documentation: https://appdoc.app/artifact/io.nextflow/nf-tower/
- License: Apache 2.0
-
Latest release: 20.10.0
published over 5 years ago
Rankings
repo1.maven.org: io.nextflow:nxf-ignite
A DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner
- Homepage: http://www.nextflow.io
- Documentation: https://appdoc.app/artifact/io.nextflow/nxf-ignite/
- License: Apache 2.0
-
Latest release: 18.10.1
published over 7 years ago
Rankings
repo1.maven.org: io.nextflow:nxf-ga4gh
A DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner
- Homepage: http://www.nextflow.io
- Documentation: https://appdoc.app/artifact/io.nextflow/nxf-ga4gh/
- License: Apache 2.0
-
Latest release: 18.10.1
published over 7 years ago
Rankings
repo1.maven.org: io.nextflow:nxf-gridgain
A DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner
- Homepage: http://www.nextflow.io
- Documentation: https://appdoc.app/artifact/io.nextflow/nxf-gridgain/
- License: GPLv3
-
Latest release: 0.15.6
published over 10 years ago
Rankings
repo1.maven.org: io.nextflow:nxf-extrae
A DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner
- Homepage: http://www.nextflow.io
- Documentation: https://appdoc.app/artifact/io.nextflow/nxf-extrae/
- License: GPLv3
-
Latest release: 0.21.3
published over 9 years ago
Rankings
repo1.maven.org: io.nextflow:nxf-google
A DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner
- Homepage: http://www.nextflow.io
- Documentation: https://appdoc.app/artifact/io.nextflow/nxf-google/
- License: Apache 2.0
-
Latest release: 18.12.0-edge
published about 7 years ago
Rankings
repo1.maven.org: io.nextflow:nxf-httpfs
A DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner
- Homepage: http://www.nextflow.io
- Documentation: https://appdoc.app/artifact/io.nextflow/nxf-httpfs/
- License: Apache 2.0
-
Latest release: 18.10.1
published over 7 years ago
Rankings
repo1.maven.org: io.nextflow:nxf-commons
A DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner
- Homepage: http://www.nextflow.io
- Documentation: https://appdoc.app/artifact/io.nextflow/nxf-commons/
- License: Apache 2.0
-
Latest release: 18.10.1
published over 7 years ago
Rankings
repo1.maven.org: io.nextflow:nxf-console
A DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner
- Homepage: http://www.nextflow.io
- Documentation: https://appdoc.app/artifact/io.nextflow/nxf-console/
- License: Apache 2.0
-
Latest release: 18.10.1
published over 7 years ago
Rankings
repo1.maven.org: io.nextflow:nxf-drmaa
A DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner
- Homepage: http://www.nextflow.io
- Documentation: https://appdoc.app/artifact/io.nextflow/nxf-drmaa/
- License: GPLv3
-
Latest release: 0.27.6
published about 8 years ago
Rankings
Dependencies
- com.amazonaws:aws-java-sdk-s3 1.11.542 implementation
- com.google.code.gson:gson 2.8.9 implementation
- ch.grengine:grengine 1.3.0 api
- ch.qos.logback:logback-classic 1.2.11 api
- ch.qos.logback:logback-core 1.2.11 api
- com.beust:jcommander 1.35 api
- com.esotericsoftware.kryo:kryo 2.24.0 api
- commons-codec:commons-codec 1.15 api
- commons-io:commons-io 2.11.0 api
- commons-lang:commons-lang 2.6 api
- dev.failsafe:failsafe 3.1.0 api
- javax.activation:activation 1.1.1 api
- javax.mail:mail 1.4.7 api
- jline:jline 2.9 api
- org.codehaus.gpars:gpars 1.2.1 api
- org.codehaus.groovy:groovy 3.0.10 api
- org.codehaus.groovy:groovy-json 3.0.10 api
- org.codehaus.groovy:groovy-nio 3.0.10 api
- org.codehaus.groovy:groovy-templates 3.0.10 api
- org.codehaus.groovy:groovy-xml 3.0.10 api
- org.eclipse.jgit:org.eclipse.jgit 6.2.0.202206071550-r api
- org.iq80.leveldb:leveldb 0.12 api
- org.jsoup:jsoup 1.14.3 api
- org.pf4j:pf4j 3.4.1 api
- org.slf4j:jcl-over-slf4j 1.7.36 api
- org.slf4j:jul-to-slf4j 1.7.36 api
- org.slf4j:log4j-over-slf4j 1.7.36 api
- org.yaml:snakeyaml 1.30 api
- org.subethamail:subethasmtp 3.1.7 testImplementation
- ch.qos.logback:logback-classic 1.2.11 api
- com.google.guava:guava 31.1-jre api
- commons-lang:commons-lang 2.6 api
- org.codehaus.groovy:groovy 3.0.10 api
- org.codehaus.groovy:groovy-nio 3.0.10 api
- org.pf4j:pf4j 3.4.1 api
- org.pf4j:pf4j-update 2.3.0 api
- ch.qos.logback:logback-classic 1.2.11 api
- com.esotericsoftware.kryo:kryo 2.24.0 api
- org.codehaus.groovy:groovy 3.0.10 api
- org.codehaus.groovy:groovy-nio 3.0.10 api
- com.github.tomakehurst:wiremock 1.57 testImplementation
- com.github.tomjankes:wiremock-groovy 0.2.0 testImplementation
- org.codehaus.groovy:groovy-json 3.0.10 testImplementation
- com.amazonaws:aws-java-sdk-batch 1.12.129 api
- com.amazonaws:aws-java-sdk-codecommit 1.12.129 api
- com.amazonaws:aws-java-sdk-ec2 1.12.129 api
- com.amazonaws:aws-java-sdk-ecs 1.12.129 api
- com.amazonaws:aws-java-sdk-iam 1.12.129 api
- com.amazonaws:aws-java-sdk-logs 1.12.129 api
- com.amazonaws:aws-java-sdk-s3 1.12.129 api
- javax.xml.bind:jaxb-api 2.3.1 api
- org.pf4j:pf4j 3.4.1 compileOnly
- org.slf4j:slf4j-api 1.7.10 compileOnly
- org.codehaus.groovy:groovy 3.0.10 testImplementation
- org.codehaus.groovy:groovy-nio 3.0.10 testImplementation
- com.azure:azure-storage-blob 12.9.0 api
- com.microsoft.azure:azure-batch 9.0.0 api
- org.pf4j:pf4j 3.4.1 compileOnly
- org.slf4j:slf4j-api 1.7.10 compileOnly
- org.codehaus.groovy:groovy 3.0.10 testImplementation
- org.codehaus.groovy:groovy-nio 3.0.10 testImplementation
- com.amazonaws:aws-java-sdk-codecommit 1.12.129 api
- javax.xml.bind:jaxb-api 2.3.1 api
- org.pf4j:pf4j 3.4.1 compileOnly
- org.slf4j:slf4j-api 1.7.10 compileOnly
- org.codehaus.groovy:groovy 3.0.10 testImplementation
- org.codehaus.groovy:groovy-nio 3.0.10 testImplementation
- org.codehaus.groovy:groovy-console 3.0.10 api
- org.codehaus.groovy:groovy-swing 3.0.10 api
- org.pf4j:pf4j 3.4.1 compileOnly
- org.slf4j:slf4j-api 1.7.10 compileOnly
- org.codehaus.groovy:groovy 3.0.10 testImplementation
- org.codehaus.groovy:groovy-nio 3.0.10 testImplementation
- com.google.code.gson:gson 2.8.9 api
- com.squareup.okhttp:logging-interceptor 2.7.5 api
- com.squareup.okhttp:okhttp 2.7.5 api
- io.swagger:swagger-annotations 1.5.15 api
- javax.annotation:javax.annotation-api 1.3.2 api
- joda-time:joda-time 2.9.9 api
- org.pf4j:pf4j 3.4.1 compileOnly
- org.slf4j:slf4j-api 1.7.10 compileOnly
- org.codehaus.groovy:groovy 3.0.10 testImplementation
- org.codehaus.groovy:groovy-nio 3.0.10 testImplementation
- com.google.apis:google-api-services-lifesciences v2beta-rev20210527-1.31.5 api
- com.google.auth:google-auth-library-oauth2-http 0.18.0 api
- com.google.cloud:google-cloud-logging 3.8.0 api
- com.google.cloud:google-cloud-nio 0.121.2 api
- org.pf4j:pf4j 3.4.1 compileOnly
- org.slf4j:slf4j-api 1.7.10 compileOnly
- org.codehaus.groovy:groovy 3.0.10 testImplementation
- org.codehaus.groovy:groovy-nio 3.0.10 testImplementation
- com.fasterxml.jackson.core:jackson-databind 2.12.5 api
- com.fasterxml.jackson.dataformat:jackson-dataformat-yaml 2.12.5 api
- org.codehaus.groovy:groovy-yaml 3.0.10 api
- org.pf4j:pf4j 3.4.1 compileOnly
- org.slf4j:slf4j-api 1.7.10 compileOnly
- org.codehaus.groovy:groovy 3.0.10 testImplementation
- org.codehaus.groovy:groovy-nio 3.0.10 testImplementation
- actions/checkout v3 composite
- actions/setup-java v3 composite
- actions/upload-artifact v3 composite
- actions/checkout v3 composite
- citation-file-format/cffconvert-github-action 2.0.0 composite
- amazoncorretto 17.0.5 build
- fluxrm/flux-sched focal build
- pditommaso/dkrbase 1.2 build
- com.google.code.gson:gson 2.9.0 api
- org.apache.commons:commons-compress 1.21 api
- org.pf4j:pf4j 3.4.1 compileOnly
- org.slf4j:slf4j-api 1.7.10 compileOnly
- org.codehaus.groovy:groovy 3.0.14 testImplementation
- org.codehaus.groovy:groovy-nio 3.0.14 testImplementation
- actions/checkout v1 composite
- actions/setup-python v4 composite
- mambaorg/micromamba 1.3.1 build
- alpine latest build
- org.pf4j:pf4j 3.4.1 compileOnly
- org.slf4j:slf4j-api 2.0.7 compileOnly
- org.codehaus.groovy:groovy 3.0.19 testImplementation
- org.codehaus.groovy:groovy-nio 3.0.19 testImplementation
- myst-parser ==0.18.1
- sphinx ==5.3.0
- sphinx-rtd-theme ==1.1.1
- sphinxcontrib-mermaid ==0.9.2