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# **Nextflow fundamentals training**
# Nextflow fundamentals training

Is your code reusable? Are your results reproducible? Tired of reinventing the wheel? The thing is that reproducibility and even repeatability is challenging even if you are very careful about keeping the same software parameters and versions. Do you want to learn how to write reusable, reproducible, and scalable pipelines?

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## Nextflow training notes

Welcome to the notes for the Nextflow training offered to the researchers of DTU - Biosustain and DTU - Bioengineering. This course is half dedicated to explain Nextflow fundamentals and half dedicated to practice Nextflow. The materials are based mostly on [Nextflow trainings portal](https://training.nextflow.io/).
Welcome to the notes for the Nextflow training offered to the researchers of DTU - Biosustain and DTU - Bioengineering. This course is half dedicated to explain Nextflow fundamentals and half dedicated to practice Nextflow. The materials are adapted from the [Nextflow trainings portal](https://training.nextflow.io/).

Please visit [About](https://biosustain.github.io/dsp_nextflow_training/about.html) to know about the course, the Data Science platform and what the course covers, go to Course Information to figure out about the details ([instructions](https://biosustain.github.io/dsp_nextflow_training/course_information/Instructions.html), [location](https://biosustain.github.io/dsp_nextflow_training/course_information/Location.html) and [timing](https://biosustain.github.io/dsp_nextflow_training/course_information/Timing.html)). Please visit Instructions first before starting the hands-on part. Once you have started your Codespace, please follow course along in the Course contents. To keep learning Nextflow and nf-core pipelines please visit [Resources](https://biosustain.github.io/dsp_nextflow_training/resources.html).
Please visit [About](https://biosustain.github.io/dsp_nextflow_training/about.html) to know about the course, the Data Science platform and what the course covers, go to Course Information to figure out about the ([instructions](https://biosustain.github.io/dsp_nextflow_training/course_information/Instructions.html), [location](https://biosustain.github.io/dsp_nextflow_training/course_information/Location.html) and [timing](https://biosustain.github.io/dsp_nextflow_training/course_information/Timing.html)). Please visit Instructions first before starting the hands-on part. Once you have started your Codespace, please follow the [tutotial](https://biosustain.github.io/dsp_nextflow_training/course_contents/Tutorial.html) in the Course contents. Running a [Real Workflow](https://biosustain.github.io/dsp_nextflow_training/course_contents/RunningRealWorkflow.html) and the use of [Seqera Platform](https://biosustain.github.io/dsp_nextflow_training/course_contents/SeqeraPlatform.html) is going to be more like a demo than hands-on but you are welcome to try to follow along with the instructors.

And remember to ask questions during the course or after the course, you can contact us at [Data Science platform email](mailto:datascience@biosustain.dtu.dk).
To keep learning Nextflow and nf-core pipelines please visit [Resources](https://biosustain.github.io/dsp_nextflow_training/resources.html).

And remember to ask questions during the course or after the course, you can always contact us at [Data Science platform email](mailto:datascience@biosustain.dtu.dk).

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<p class="prev-next-subtitle">previous</p>
<p class="prev-next-title"><strong>Nextflow fundamentals training</strong></p>
<p class="prev-next-title">Nextflow fundamentals training</p>
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Expand Up @@ -344,15 +344,16 @@ <h2> Contents </h2>
<article class="bd-article">

<section class="tex2jax_ignore mathjax_ignore" id="nextflow-fundamentals-training">
<h1><strong>Nextflow fundamentals training</strong><a class="headerlink" href="#nextflow-fundamentals-training" title="Link to this heading">#</a></h1>
<h1>Nextflow fundamentals training<a class="headerlink" href="#nextflow-fundamentals-training" title="Link to this heading">#</a></h1>
<p>Is your code reusable? Are your results reproducible? Tired of reinventing the wheel? The thing is that reproducibility and even repeatability is challenging even if you are very careful about keeping the same software parameters and versions. Do you want to learn how to write reusable, reproducible, and scalable pipelines?</p>
<p><strong>Nextflow</strong> is an advanced workflow management system designed to streamline data-driven processes, especially in the bioinformatics and computational biology fields. It allows users to develop, to execute, and to scale complex workflows across various environments (i.e local machine, Cloud - Azure, AWS, etc… - or HPC). This system is simple and flexible and supports different programming languages (i.e. Python, R, Bash) and containers (e.g Docker, Singularity, etc…).</p>
<p>Let us introduce you to Nextflow and unlock you a door to a vibrant community building and maintaining standardized reproducible bioinformatics analyses, trainings, hackathons and resources to make your data-driven analysis scalable an reproducible.</p>
<section id="nextflow-training-notes">
<h2>Nextflow training notes<a class="headerlink" href="#nextflow-training-notes" title="Link to this heading">#</a></h2>
<p>Welcome to the notes for the Nextflow training offered to the researchers of DTU - Biosustain and DTU - Bioengineering. This course is half dedicated to explain Nextflow fundamentals and half dedicated to practice Nextflow. The materials are based mostly on <a class="reference external" href="https://training.nextflow.io/" rel="noopener noreferrer" target="_blank">Nextflow trainings portal</a>.</p>
<p>Please visit <a class="reference external" href="https://biosustain.github.io/dsp_nextflow_training/about.html" rel="noopener noreferrer" target="_blank">About</a> to know about the course, the Data Science platform and what the course covers, go to Course Information to figure out about the details (<a class="reference external" href="https://biosustain.github.io/dsp_nextflow_training/course_information/Instructions.html" rel="noopener noreferrer" target="_blank">instructions</a>, <a class="reference external" href="https://biosustain.github.io/dsp_nextflow_training/course_information/Location.html" rel="noopener noreferrer" target="_blank">location</a> and <a class="reference external" href="https://biosustain.github.io/dsp_nextflow_training/course_information/Timing.html" rel="noopener noreferrer" target="_blank">timing</a>). Please visit Instructions first before starting the hands-on part. Once you have started your Codespace, please follow course along in the Course contents. To keep learning Nextflow and nf-core pipelines please visit <a class="reference external" href="https://biosustain.github.io/dsp_nextflow_training/resources.html" rel="noopener noreferrer" target="_blank">Resources</a>.</p>
<p>And remember to ask questions during the course or after the course, you can contact us at <a class="reference external" href="mailto:datascience&#37;&#52;&#48;biosustain&#46;dtu&#46;dk" rel="noopener noreferrer" target="_blank">Data Science platform email</a>.</p>
<p>Welcome to the notes for the Nextflow training offered to the researchers of DTU - Biosustain and DTU - Bioengineering. This course is half dedicated to explain Nextflow fundamentals and half dedicated to practice Nextflow. The materials are adapted from the <a class="reference external" href="https://training.nextflow.io/" rel="noopener noreferrer" target="_blank">Nextflow trainings portal</a>.</p>
<p>Please visit <a class="reference external" href="https://biosustain.github.io/dsp_nextflow_training/about.html" rel="noopener noreferrer" target="_blank">About</a> to know about the course, the Data Science platform and what the course covers, go to Course Information to figure out about the (<a class="reference external" href="https://biosustain.github.io/dsp_nextflow_training/course_information/Instructions.html" rel="noopener noreferrer" target="_blank">instructions</a>, <a class="reference external" href="https://biosustain.github.io/dsp_nextflow_training/course_information/Location.html" rel="noopener noreferrer" target="_blank">location</a> and <a class="reference external" href="https://biosustain.github.io/dsp_nextflow_training/course_information/Timing.html" rel="noopener noreferrer" target="_blank">timing</a>). Please visit Instructions first before starting the hands-on part. Once you have started your Codespace, please follow the <a class="reference external" href="https://biosustain.github.io/dsp_nextflow_training/course_contents/Tutorial.html" rel="noopener noreferrer" target="_blank">tutotial</a> in the Course contents. Running a <a class="reference external" href="https://biosustain.github.io/dsp_nextflow_training/course_contents/RunningRealWorkflow.html" rel="noopener noreferrer" target="_blank">Real Workflow</a> and the use of <a class="reference external" href="https://biosustain.github.io/dsp_nextflow_training/course_contents/SeqeraPlatform.html" rel="noopener noreferrer" target="_blank">Seqera Platform</a> is going to be more like a demo than hands-on but you are welcome to try to follow along with the instructors.</p>
<p>To keep learning Nextflow and nf-core pipelines please visit <a class="reference external" href="https://biosustain.github.io/dsp_nextflow_training/resources.html" rel="noopener noreferrer" target="_blank">Resources</a>.</p>
<p>And remember to ask questions during the course or after the course, you can always contact us at <a class="reference external" href="mailto:datascience&#37;&#52;&#48;biosustain&#46;dtu&#46;dk" rel="noopener noreferrer" target="_blank">Data Science platform email</a>.</p>
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