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Goodbye GitPod, hello GitHub Codespaces.
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README.md

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## » <https://training.nextflow.io> «
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[![Open in GitPod](https://img.shields.io/badge/Gitpod-%20Open%20in%20Gitpod-908a85?logo=gitpod)](https://gitpod.io/#https://github.com/nextflow-io/training)
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[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/nextflow-io/training?quickstart=1&ref=master)
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Welcome to the Nextflow training repository!
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We are excited to have you on the path to writing reproducible and scalable scientific workflows using Nextflow.
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- 👉🏻 Written training material: <https://training.nextflow.io>
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- 👩🏻‍💻 Instructions on loading this repository within a GitPod environment: <https://training.nextflow.io/envsetup/>
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- 👩🏻‍💻 Instructions on loading this repository within a GitHub Codespaces environment: <https://training.nextflow.io/envsetup/>
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- 📚 Nextflow documentation: <https://www.nextflow.io/docs/latest/>
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docs/advanced/index.md

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Let's get started!
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[![Open in Gitpod](https://img.shields.io/badge/Gitpod-%20Open%20in%20Gitpod-908a85?logo=gitpod)](https://gitpod.io/#https://github.com/nextflow-io/training)
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[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/nextflow-io/training?quickstart=1&ref=master)
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## Learning objectives
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docs/advanced/orientation.md

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# Orientation
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The Gitpod environment contains some test data that will be used in this workshop.
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The GitHub Codespaces environment contains some test data that will be used in this workshop.
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!!! note
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Follow [this link](../envsetup/index.md) if you have not yet setup your Gitpod environment.
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Follow [this link](../envsetup/index.md) if you have not yet setup your GitHub Codespaces environment.
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## Getting started
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docs/basic_training/containers.md

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Conda is a popular package and environment manager. The built-in support for Conda allows Nextflow workflows to automatically create and activate the Conda environment(s), given the dependencies specified by each process.
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In this Gitpod environment, conda is already installed.
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In this GitHub Codespaces environment, conda is already installed.
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### Using conda
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docs/basic_training/index.md

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Let's get started!
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[![Open in Gitpod](https://img.shields.io/badge/Gitpod-%20Open%20in%20Gitpod-908a85?logo=gitpod)](https://gitpod.io/#https://github.com/nextflow-io/training)
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[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/nextflow-io/training?quickstart=1&ref=master)
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## Learning objectives
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docs/basic_training/orientation.md

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# Orientation
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The Gitpod environment contains some test data that will be used in this workshop.
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The GitHub Codespaces environment contains some test data that will be used in this workshop.
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!!! note
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Follow [this link](../envsetup/index.md) if you have not yet setup your Gitpod environment.
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Follow [this link](../envsetup/index.md) if you have not yet setup your GitHub Codespaces environment.
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## Getting started
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docs/basic_training/setup.fr.md

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La seconde consiste à utiliser [Gitpod](#gitpod), ce qui est préférable pour les débutants car cette plateforme contient tous les programmes et données nécessaires. Il suffit de cliquer sur le lien et de se connecter à l'aide de son compte GitHub pour commencer le tutoriel :
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[![Open in Gitpod](https://img.shields.io/badge/Gitpod-%20Open%20in%20Gitpod-908a85?logo=gitpod)](https://gitpod.io/#https://github.com/nextflow-io/training)
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[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/nextflow-io/training?quickstart=1&ref=master)
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## Installation locale
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docs/basic_training/setup.pt.md

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A segunda é usar o [Gitpod](#gitpod), o que é melhor para iniciantes, pois esta plataforma contém todos os programas e dados necessários. Basta clicar no link abaixo e fazer login usando sua conta do GitHub para iniciar o tutorial:
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[![Abra no Gitpod](https://img.shields.io/badge/Gitpod-%20Abra%20no%20Gitpod-908a85?logo=gitpod)](https://gitpod.io/#https://github.com/nextflow-io/training)
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[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/nextflow-io/training?quickstart=1&ref=master)
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## Instalação local
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docs/envsetup/01_setup.md

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# Gitpod
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# GitHub Codespaces
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Gitpod is a cloud development environment for teams to efficiently and securely develop software. It can improve your developer experience by coding in a cloud development environment.
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GitHub Codespaces is a cloud development environment for teams to efficiently and securely develop software. It can improve your developer experience by coding in a cloud development environment.
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## Creating a Gitpod account
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You can create a free [Gitpod](https://gitpod.io/) account using your GitLab, GitHub, or Bitbucket account.
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You can create a free GitHub account from the [GitHub home page](https://github.com/).
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You can create an account using the [Gitpod login page](https://gitpod.io/login/).
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## Running GitHub Codespaces
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![Gitpod log in](img/login.png)
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Once you are logged in to GitHub, open this link in your browser to open the training environment: <https://codespaces.new/nextflow-io/training?quickstart=1&ref=master>
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It is best to connect your LinkedIn account to receive a full 50 hours usage allocation.
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Alternatively, you can click on the button below.
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![Gitpod log in one step](img/onestepaway.png)
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[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/nextflow-io/training?quickstart=1&ref=master)
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After selecting your preferred editor, theme, and profile details, click continue and your account will be created and ready to use.
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You should be presented with a page where you can create a new GitHub Codespace:
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!!! note
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![Create a GitHub Codespace](img/codespaces_create.png)
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It is recommended to use the VS code editor.
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If you wish, you can click "Change options" to configure the machine used, though the defaults should be fine.
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## Running Gitpod
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!!! warning
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Click the following URL to run Gitpod: <https://gitpod.io/#https://github.com/nextflow-io/training>
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Opening a new GitHub Codespaces environment for the first time can take several minutes.
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It's worth grabbing a cup of tea and checking your emails.
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This URL is the Nextflow training repository prefixed with `https://gitpod.io/#`.
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## Explore your GitHub Codespaces IDE
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Alternatively, you can click on the button below.
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After GitHub Codespaces has loaded, you should see something similar to the following (which may in light mode depending on your account preferences):
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[![Open Gitpod](https://img.shields.io/badge/Gitpod-%20Open%20in%20Gitpod-908a85?logo=gitpod)](https://gitpod.io/#https://github.com/nextflow-io/training)
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![GitHub Codespaces welcome](img/codespaces_welcome.png)
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If you are already logged in, your Gitpod environment will start to load.
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This is the interface of the VSCode IDE, a popular code development application that we recommend using for Nextflow development.
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### Explore your Gitpod IDE
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- **The sidebar** allows you to customize your GitHub Codespaces environment and perform basic tasks (copy, paste, open files, search, git, etc.). You can click the explorer button to see which files are in this repository.
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- **The terminal** allows you to run all the programs in the repository. For example, both `nextflow` and `docker` are installed and can be executed.
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- **The file explorer** allows you to view and edit files. Clicking on a file in the explorer will open it within the main window.
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- **The main editor** showing you a preview of the `README.md` file.
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After Gitpod has loaded, you should see something similar to the following:
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## Reopening a GitHub Codespaces session
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![Gitpod welcome](img/gitpod.welcome.png)
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Once you have created an envionrment, you can easily resume or restart it and continue from where you left off.
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- **The sidebar** allows you to customize your Gitpod environment and perform basic tasks (copy, paste, open files, search, git, etc.). You can click the explorer button to see which files are in this repository.
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- **The terminal** allows you to run all the programs in the repository. For example, both `nextflow` and `docker` are installed and can be executed.
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- **The file explorer** allows you to view and edit files. Clicking on a file in the explorer will open it within the main window.
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- **The Simple Browser** lets you view the nf-training material browser (<https://training.nextflow.io/>). If you close it by accident, you can load the simple browser again by typing the following in the terminal: `gp preview https://training.nextflow.io`.
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You can reopen an environment from <https://github.com/codespaces/>. Previous environments will be listed. Click a session to resume it.
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### Gitpod resources
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![List GitHub Codespace sessions](img/codespaces_list.png)
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Gitpod gives you 500 free credits per month, which is equivalent to 50 hours of free environment runtime using the standard workspace (up to 4 cores, 8 GB RAM, and 30 GB storage).
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If you have saved the URL for your previous Gitpod environment, you can simply open it in your browser.
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There is also a large workspace option that gives you up to 8 cores, 16GB RAM, and 50GB storage. However, the large workspace will use your free credits quicker and you will have fewer hours of access to this space.
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Alternatively, click the same button that you used to create it in the first place:
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Gitpod will time out after 30 minutes of inactivity and will save your changes for up to 2 weeks.
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[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/nextflow-io/training?quickstart=1&ref=master)
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More information about Gitpod is available at [gitpod.io](https://www.gitpod.io).
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You should see the previous session, the default option is to resume it:
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### Reopening a Gitpod session
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![Resume a GitHub Codespace](img/codespaces_resume.png)
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You can reopen an environment from <https://gitpod.io/workspaces>. Previous environments will be listed. You can select the ellipsis (three dots icon) and then select `Open` to reopen a previous environment.
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## GitHub Codespaces billing
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If you have saved the URL for your previous Gitpod environment, you can simply open it in your browser.
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GitHub Codespaces gives you up to 15 GB-month storage per month, and 120 core-hours per month.
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This is equivalent to around 60 hours of free environment runtime using the standard workspace (up to 2 cores, 8 GB RAM, and 32 GB storage).
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GitHub Codespaces environments are configurable. You can create them with more resources, but this will use your free usage quicker and you will have fewer hours of access to this space.
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GitHub Codespaces will time out after 30 minutes of inactivity and will save your changes for up to 2 weeks.
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Alternatively, you can open a new training workspace by following the Gitpod URL: <https://gitpod.io/#https://github.com/nextflow-io/training>
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More information can be found in the GitHub docs:
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[About billing for GitHub Codespaces](https://docs.github.com/en/billing/managing-billing-for-your-products/managing-billing-for-github-codespaces/about-billing-for-github-codespaces)
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### Saving files from Gitpod to your local machine
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### Saving files from GitHub Codespaces to your local machine
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To save any file from the explorer panel, right-click the file and select `Download`.

docs/envsetup/01_setup.pt.md

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Você também pode acessar o material clicando no botão abaixo.
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[![Open Gitpod](https://img.shields.io/badge/Gitpod-%20Open%20in%20Gitpod-908a85?logo=gitpod)](https://gitpod.io/#https://github.com/nextflow-io/training)
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[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/nextflow-io/training?quickstart=1&ref=master)
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Se você já estiver logado, seu ambiente no Gitpod começará a carregar.
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