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Repository files navigation

Nextflow Logo

"Dataflow variables are spectacularly expressive in concurrent programming"
Henri E. Bal , Jennifer G. Steiner , Andrew S. Tanenbaum

Nextflow CINextflow versionNextflow TwitterNextflow Publicationinstall with biocondaNextflow license

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:

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:

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, 316–319 (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.

About

A DSL for data-driven computational pipelines

nextflow.io

Resources

Readme
License

Code of conduct

Code of conduct

Contributing

Contributing
Activity
Custom properties

Stars

0 stars

Watchers

0 watching

Forks

0 forks
Report repository

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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

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CODE-OF-CONDUCT.md
CONTRIBUTING.md
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settings.gradle
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Repository files navigation
Nextflow Logo
"Dataflow variables are spectacularly expressive in concurrent programming"
Henri E. Bal , Jennifer G. Steiner , Andrew S. Tanenbaum
Nextflow CINextflow versionNextflow TwitterNextflow Publicationinstall with biocondaNextflow license
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:
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:
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, 316–319 (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.
About
A DSL for data-driven computational pipelines
nextflow.io
Resources
Readme
License
Code of conduct
Code of conduct
Contributing
Contributing
Activity
Custom properties
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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tests
tests
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validation
.codespellrc
.codespellrc
.editorconfig
.editorconfig
.gitignore
.gitignore
CITATION.cff
CITATION.cff
CODE-OF-CONDUCT.md
CODE-OF-CONDUCT.md
CONTRIBUTING.md
CONTRIBUTING.md
COPYING
COPYING
GIT-README.md
GIT-README.md
Makefile
Makefile
NOTICE
NOTICE
README.md
README.md
VERSION
VERSION
build.gradle
build.gradle
changelog.txt
changelog.txt
compile.sh
compile.sh
console.sh
console.sh
gradle.properties
gradle.properties
gradlew
gradlew
gradlew.bat
gradlew.bat
launch.sh
launch.sh
nextflow
nextflow
nextflow.md5
nextflow.md5
nextflow.sha1
nextflow.sha1
nextflow.sha256
nextflow.sha256
packing.gradle
packing.gradle
profile.sh
profile.sh
settings.gradle
settings.gradle
test-ci.sh
test-ci.sh
Repository files navigation
Nextflow Logo
"Dataflow variables are spectacularly expressive in concurrent programming"
Henri E. Bal , Jennifer G. Steiner , Andrew S. Tanenbaum
Nextflow CINextflow versionNextflow TwitterNextflow Publicationinstall with biocondaNextflow license
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:
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:
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, 316–319 (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.
About
A DSL for data-driven computational pipelines
nextflow.io
Resources
Readme
License
Code of conduct
Code of conduct
Contributing
Contributing
Activity
Custom properties
Stars
0 stars
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0 watching
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0 forks
Report repository
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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modules
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plugins
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tests
tests
validation
validation
.codespellrc
.codespellrc
.editorconfig
.editorconfig
.gitignore
.gitignore
CITATION.cff
CITATION.cff
CODE-OF-CONDUCT.md
CODE-OF-CONDUCT.md
CONTRIBUTING.md
CONTRIBUTING.md
COPYING
COPYING
GIT-README.md
GIT-README.md
Makefile
Makefile
NOTICE
NOTICE
README.md
README.md
VERSION
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build.gradle
build.gradle
changelog.txt
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compile.sh
compile.sh
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gradle.properties
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gradlew
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launch.sh
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nextflow
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nextflow.md5
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nextflow.sha1
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nextflow.sha256
nextflow.sha256
packing.gradle
packing.gradle
profile.sh
profile.sh
settings.gradle
settings.gradle
test-ci.sh
test-ci.sh
Repository files navigation
Nextflow Logo
"Dataflow variables are spectacularly expressive in concurrent programming"
Henri E. Bal , Jennifer G. Steiner , Andrew S. Tanenbaum
Nextflow CINextflow versionNextflow TwitterNextflow Publicationinstall with biocondaNextflow license
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:
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:
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, 316–319 (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.
About
A DSL for data-driven computational pipelines
nextflow.io
Resources
Readme
License
Code of conduct
Code of conduct
Contributing
Contributing
Activity
Custom properties
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

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.codespellrc
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.editorconfig
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.gitignore
.gitignore
CITATION.cff
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CODE-OF-CONDUCT.md
CODE-OF-CONDUCT.md
CONTRIBUTING.md
CONTRIBUTING.md
COPYING
COPYING
GIT-README.md
GIT-README.md
Makefile
Makefile
NOTICE
NOTICE
README.md
README.md
VERSION
VERSION
build.gradle
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compile.sh
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console.sh
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gradle.properties
gradle.properties
gradlew
gradlew
gradlew.bat
gradlew.bat
launch.sh
launch.sh
nextflow
nextflow
nextflow.md5
nextflow.md5
nextflow.sha1
nextflow.sha1
nextflow.sha256
nextflow.sha256
packing.gradle
packing.gradle
profile.sh
profile.sh
settings.gradle
settings.gradle
test-ci.sh
test-ci.sh
Repository files navigation
Nextflow Logo
"Dataflow variables are spectacularly expressive in concurrent programming"
Henri E. Bal , Jennifer G. Steiner , Andrew S. Tanenbaum
Nextflow CINextflow versionNextflow TwitterNextflow Publicationinstall with biocondaNextflow license
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:
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:
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, 316–319 (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.
About
A DSL for data-driven computational pipelines
nextflow.io
Resources
Readme
License
Code of conduct
Code of conduct
Contributing
Contributing
Activity
Custom properties
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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CONTRIBUTING.md
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Repository files navigation
Nextflow Logo
"Dataflow variables are spectacularly expressive in concurrent programming"
Henri E. Bal , Jennifer G. Steiner , Andrew S. Tanenbaum
Nextflow CINextflow versionNextflow TwitterNextflow Publicationinstall with biocondaNextflow license
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:
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:
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, 316–319 (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.
About
A DSL for data-driven computational pipelines
nextflow.io
Resources
Readme
License
Code of conduct
Code of conduct
Contributing
Contributing
Activity
Custom properties
Stars
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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Repository files navigation
Nextflow Logo
"Dataflow variables are spectacularly expressive in concurrent programming"
Henri E. Bal , Jennifer G. Steiner , Andrew S. Tanenbaum
Nextflow CINextflow versionNextflow TwitterNextflow Publicationinstall with biocondaNextflow license
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:
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:
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, 316–319 (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.
About
A DSL for data-driven computational pipelines
nextflow.io
Resources
Readme
License
Code of conduct
Code of conduct
Contributing
Contributing
Activity
Custom properties
Stars
0 stars
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0 watching
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0 forks
Report repository
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

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.codespellrc
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.editorconfig
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CODE-OF-CONDUCT.md
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GIT-README.md
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compile.sh
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Repository files navigation
Nextflow Logo
"Dataflow variables are spectacularly expressive in concurrent programming"
Henri E. Bal , Jennifer G. Steiner , Andrew S. Tanenbaum
Nextflow CINextflow versionNextflow TwitterNextflow Publicationinstall with biocondaNextflow license
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:
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:
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, 316–319 (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.
About
A DSL for data-driven computational pipelines
nextflow.io
Resources
Readme
License
Code of conduct
Code of conduct
Contributing
Contributing
Activity
Custom properties
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages