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Improve getting started docs (#4764) [ci skip]
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Signed-off-by: Justine Geffen <justinegeffen@users.noreply.github.com>
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Co-authored-by: Ben Sherman <bentshermann@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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3 people committed Mar 20, 2024
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2 changes: 2 additions & 0 deletions docs/conf.py
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myst_heading_anchors = 3

rediraffe_redirects = {
'basic.md': 'overview.md',
'getstarted.md': 'install.md',
'dsl2.md': 'dsl1.md'
}

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2 changes: 1 addition & 1 deletion docs/developer/index.md
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### Groovy REPL

The `groovysh` command provides a command-line REPL that you can use to play around with Groovy code independently of Nextflow. The `groovyConsole` command provides a graphical REPL similar to `nextflow console`. These commands require a standalone Groovy distribution, which can be installed as described for Java in {ref}`Getting started <getstarted-requirement>`.
The `groovysh` command provides a command-line REPL that you can use to play around with Groovy code independently of Nextflow. The `groovyConsole` command provides a graphical REPL similar to `nextflow console`. These commands require a standalone Groovy distribution, which can be installed as described for Java in {ref}`Getting started <install-requirements>`.

:::{note}
If you are using WSL, you must also install an X server for Windows, such as [VcXsrv](https://sourceforge.net/projects/vcxsrv/) or [Xming](http://www.straightrunning.com/XmingNotes/), in order to use these commands.
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2 changes: 1 addition & 1 deletion docs/developer/nextflow.ast.md
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3. Execute the script
4. Go to **Script** > **Inspect AST**

Here is the example from {ref}`getstarted-first`:
Here is the example from {ref}`your-first-script`:

```groovy
params.str = 'Hello world!'
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2 changes: 1 addition & 1 deletion docs/dsl1.md
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## Processes and workflows

In DSL1, a process definition is also the process invocation. Process inputs and outputs are connected to channels using `from` and `into`. Here is the {ref}`getstarted-first` example written in DSL1:
In DSL1, a process definition is also the process invocation. Process inputs and outputs are connected to channels using `from` and `into`. Here is the {ref}`your-first-script` example written in DSL1:

```groovy
nextflow.enable.dsl=1
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211 changes: 0 additions & 211 deletions docs/getstarted.md

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19 changes: 7 additions & 12 deletions docs/index.md
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# Nextflow's documentation!
# Nextflow reference documentation

[![Nextflow CI](https://github.com/nextflow-io/nextflow/workflows/Nextflow%20CI/badge.svg)](https://github.com/nextflow-io/nextflow/actions/workflows/build.yml?query=branch%3Amaster+event%3Apush)
[![Nextflow version](https://img.shields.io/github/release/nextflow-io/nextflow.svg?colorB=58bd9f&style=popout)](https://github.com/nextflow-io/nextflow/releases/latest)
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Nextflow is a workflow system for creating scalable, portable, and reproducible workflows.

## Rationale

The rise of big data has made it increasingly necessary to be able to analyze and perform experiments on large datasets in a portable and reproducible manner.

Parallelization and distributed computing are the best ways to tackle this challenge, but the tools commonly available to computational scientists often lack good support for these techniques, or they provide a model that fits poorly with the needs of computational scientists and often require knowledge of complex tools and APIs.

The Nextflow language is inspired by [the Unix philosophy](https://en.wikipedia.org/wiki/Unix_philosophy), in which many simple command line tools can be chained together into increasingly complex tasks. Similarly, a Nextflow script consists of composing many simple processes into increasingly complex pipelines. Each process executes a given tool or scripting language, and by specifying the process inputs and outputs, Nextflow coordinates the execution of tasks for you.

The Nextflow runtime integrates with many popular execution platforms (HPC schedulers, cloud providers) and software tools (Git, Docker, Conda), allowing you to fully describe a computational pipeline with all of its dependencies and run it in nearly any environment -- write once, run anywhere.
- Get an {ref}`overview <overview-page>` of Nextflow and its key concepts.
- Get started with Nextflow by {ref}`installing <install-page>` it and running {ref}`your first script <your-first-script>`.
- Check out [this blog post](https://www.nextflow.io/blog/2023/learn-nextflow-in-2023.html) for even more resources on how to learn Nextflow.

```{toctree}
:hidden:
:caption: Introduction
:maxdepth: 1
getstarted
basic
overview
install
your-first-script
```

```{toctree}
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