nextflow-io · ewels · Feb 18, 2025 · Feb 17, 2025 · Feb 17, 2025 · Feb 17, 2025
diff --git a/.github/workflows/release-docs.yml b/.github/workflows/release-docs.yml
@@ -13,10 +13,21 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
+
       - uses: actions/setup-python@v5
         with:
           python-version: 3.10.6
+
       - name: Install Dependencies
         run: pip install -r requirements.txt
+
       - name: Build Docs Website
-        run: mike deploy --push --alias-type copy --update-aliases ${{ github.event.release.tag_name }} latest
+        run: mike deploy --alias-type copy --update-aliases ${{ github.event.release.tag_name }} latest
+
+      - name: Pin GitHub Codespaces version
+        run: |
+          git checkout gh-pages
+          find ${{ github.event.release.tag_name }} -type f -exec sed -i 's|ref=master|ref=${{ github.event.release.tag_name }}|g' {} +
+          find latest -type f -exec sed -i 's|ref=master|ref=${{ github.event.release.tag_name }}|g' {} +
+          git commit -am "Pin GitHub Codespaces link versions"
+          git push
diff --git a/README.md b/README.md
@@ -2,14 +2,14 @@
 
 ## » <https://training.nextflow.io> «
 
-[![Open in GitPod](https://img.shields.io/badge/Gitpod-%20Open%20in%20Gitpod-908a85?logo=gitpod)](https://gitpod.io/#https://github.com/nextflow-io/training)
+[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/nextflow-io/training?quickstart=1&ref=master)
 
 Welcome to the Nextflow training repository!
 We are excited to have you on the path to writing reproducible and scalable scientific workflows using Nextflow.
 
 - 👉🏻 Written training material: <https://training.nextflow.io>
 
-- 👩🏻‍💻 Instructions on loading this repository within a GitPod environment: <https://training.nextflow.io/envsetup/>
+- 👩🏻‍💻 Instructions on loading this repository within a GitHub Codespaces environment: <https://training.nextflow.io/envsetup/>
 
 - 📚 Nextflow documentation: <https://www.nextflow.io/docs/latest/>
 

diff --git a/docs/advanced/index.md b/docs/advanced/index.md
@@ -10,7 +10,7 @@ By the end of this workshop, you will have the skills and knowledge to create co
 
 Let's get started!
 
-[![Open in Gitpod](https://img.shields.io/badge/Gitpod-%20Open%20in%20Gitpod-908a85?logo=gitpod)](https://gitpod.io/#https://github.com/nextflow-io/training)
+[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/nextflow-io/training?quickstart=1&ref=master)
 
 ## Learning objectives
 

diff --git a/docs/advanced/orientation.md b/docs/advanced/orientation.md
@@ -1,10 +1,10 @@
 # Orientation
 
-The Gitpod environment contains some test data that will be used in this workshop.
+The GitHub Codespaces environment contains some test data that will be used in this workshop.
 
 !!! note
 
-    Follow [this link](../envsetup/index.md) if you have not yet setup your Gitpod environment.
+    Follow [this link](../envsetup/index.md) if you have not yet setup your GitHub Codespaces environment.
 
 ## Getting started
 

diff --git a/docs/advanced/structure.md b/docs/advanced/structure.md
@@ -92,7 +92,7 @@ You'll notice a `nxf_container_env` bash function that appends our bin directory
 ```bash
 nxf_container_env() {
 cat << EOF
-export PATH="\$PATH:/workspace/gitpod/nf-training/advanced/structure/bin"
+export PATH="\$PATH:/workspaces/training/nf-training-advanced/structure/bin"
 EOF
 }
 ```

diff --git a/docs/basic_training/cache_and_resume.fr.md b/docs/basic_training/cache_and_resume.fr.md
@@ -3,6 +3,13 @@ titre: Cache et reprise
 description: Atelier de formation de base Nextflow
 ---
 
+!!! warning
+
+    Some of the translations on the training portal are out of date.
+    The translated material may be incomplete or incorrect.
+    We plan to update the translations later this year.
+    In the meantime, please try to work through the English-language material if you can.
+
 # Cache d'exécution et reprise
 
 Le mécanisme de mise en cache de Nextflow fonctionne en attribuant un identifiant unique à chaque tâche qui est utilisé pour créer un répertoire d'exécution distinct où les tâches sont exécutées et les résultats stockés.

diff --git a/docs/basic_training/cache_and_resume.pt.md b/docs/basic_training/cache_and_resume.pt.md
@@ -3,6 +3,13 @@ title: Cache e reentrância
 description: Material de treinamento básico do Nextflow
 ---
 
+!!! warning
+
+    Some of the translations on the training portal are out of date.
+    The translated material may be incomplete or incorrect.
+    We plan to update the translations later this year.
+    In the meantime, please try to work through the English-language material if you can.
+
 # Execução de cache e de reentrância
 
 O mecanismo de caching do Nextflow funciona atribuindo uma ID única para cada tarefa que é usada para criar um diretório de execução separado onde as tarefas são executadas e os resultados guardados.

diff --git a/docs/basic_training/channels.md b/docs/basic_training/channels.md
@@ -324,9 +324,9 @@ Channel
 It will produce an output similar to the following:
 
 ```console title="Output"
-[liver, [/workspace/gitpod/nf-training/data/ggal/liver_1.fq, /workspace/gitpod/nf-training/data/ggal/liver_2.fq]]
-[gut, [/workspace/gitpod/nf-training/data/ggal/gut_1.fq, /workspace/gitpod/nf-training/data/ggal/gut_2.fq]]
-[lung, [/workspace/gitpod/nf-training/data/ggal/lung_1.fq, /workspace/gitpod/nf-training/data/ggal/lung_2.fq]]
+[liver, [/workspaces/training/nf-training/data/ggal/liver_1.fq, /workspaces/training/nf-training/data/ggal/liver_2.fq]]
+[gut, [/workspaces/training/nf-training/data/ggal/gut_1.fq, /workspaces/training/nf-training/data/ggal/gut_2.fq]]
+[lung, [/workspaces/training/nf-training/data/ggal/lung_1.fq, /workspaces/training/nf-training/data/ggal/lung_2.fq]]
 ```
 
 !!! warning

diff --git a/docs/basic_training/channels.pt.md b/docs/basic_training/channels.pt.md
@@ -2,6 +2,13 @@
 description: Material de treinamento básico do Nextflow
 ---
 
+!!! warning
+
+    Some of the translations on the training portal are out of date.
+    The translated material may be incomplete or incorrect.
+    We plan to update the translations later this year.
+    In the meantime, please try to work through the English-language material if you can.
+
 # Canais
 
 Canais são uma estrutura de dados chave do Nextflow que permite a implementação de fluxos de trabalho computacionais utilizando paradigmas funcional e reativo com base no paradigma de programação [Dataflow](https://en.wikipedia.org/wiki/Dataflow_programming).
@@ -229,9 +236,9 @@ Channel
 Ele produzirá uma saída semelhante à seguinte:
 
 ```groovy
-[liver, [/workspace/gitpod/nf-training/data/ggal/liver_1.fq, /workspace/gitpod/nf-training/data/ggal/liver_2.fq]]
-[gut, [/workspace/gitpod/nf-training/data/ggal/gut_1.fq, /workspace/gitpod/nf-training/data/ggal/gut_2.fq]]
-[lung, [/workspace/gitpod/nf-training/data/ggal/lung_1.fq, /workspace/gitpod/nf-training/data/ggal/lung_2.fq]]
+[liver, [/workspaces/training/nf-training/data/ggal/liver_1.fq, /workspaces/training/nf-training/data/ggal/liver_2.fq]]
+[gut, [/workspaces/training/nf-training/data/ggal/gut_1.fq, /workspaces/training/nf-training/data/ggal/gut_2.fq]]
+[lung, [/workspaces/training/nf-training/data/ggal/lung_1.fq, /workspaces/training/nf-training/data/ggal/lung_2.fq]]
 ```
 
 !!! warning
@@ -487,7 +494,7 @@ for (List linha : linhas) {
         Adicione um arquivo de texto CSV contendo o seguinte, como uma entrada de exemplo com o nome "fastq.csv":
 
         ```csv
-        gut,/workspace/gitpod/nf-training/data/ggal/gut_1.fq,/workspace/gitpod/nf-training/data/ggal/gut_2.fq
+        gut,/workspaces/training/nf-training/data/ggal/gut_1.fq,/workspaces/training/nf-training/data/ggal/gut_2.fq
         ```
 
         Em seguida, substitua o canal de entrada para as leituras em `script7.nf`, alterando as seguintes linhas:

diff --git a/docs/basic_training/config.pt.md b/docs/basic_training/config.pt.md
@@ -3,6 +3,13 @@ title: Configuração
 description: Material de treinamento básico do Nextflow
 ---
 
+!!! warning
+
+    Some of the translations on the training portal are out of date.
+    The translated material may be incomplete or incorrect.
+    We plan to update the translations later this year.
+    In the meantime, please try to work through the English-language material if you can.
+
 # Configuração do Nextflow
 
 Um recurso importante do Nextflow é a capacidade de desacoplar a implementação do fluxo de trabalho e as configurações exigidas pela plataforma onde ele será executado.

diff --git a/docs/basic_training/containers.md b/docs/basic_training/containers.md
@@ -126,7 +126,7 @@ docker images
 
     ??? Solution
 
-        Use your favorite editor (e.g., `vim` or `nano`) to create a file named `Dockerfile`. Alternatively, run `code Dockerfile` to create a a file named `Dockerfile` in Gitpod. Copy the following content:
+        Use your favorite editor (e.g., `vim` or `nano`) to create a file named `Dockerfile`. Alternatively, run `code Dockerfile` to create a a file named `Dockerfile`. Copy the following content:
 
         ```dockerfile linenums="1" title="Dockerfile"
         FROM debian:bullseye-slim
@@ -248,7 +248,7 @@ docker run --volume $PWD:$PWD --workdir $PWD my-image \
 Or set a folder you want to mount as an environmental variable, called `DATA`:
 
 ```bash
-DATA=/workspace/gitpod/nf-training/data
+DATA=/workspaces/training/nf-training/data
 docker run --volume $DATA:$DATA --workdir $PWD my-image \
     salmon index -t $PWD/data/ggal/transcriptome.fa -i transcript-index
 ```
@@ -429,7 +429,7 @@ In the same way that you can push Docker images to Docker Hub, you can upload Si
 
 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.
 
-In this Gitpod environment, conda is already installed.
+In this GitHub Codespaces environment, conda is already installed.
 
 ### Using conda
 
@@ -624,7 +624,7 @@ mulled-search --destination quay singularity --channel bioconda --search bowtie
 
 !!! question "Exercise"
 
-    During the earlier RNA-Seq tutorial (script2.nf), you created an index with the salmon tool. Given you do not have salmon installed locally in the machine provided by Gitpod, you had to either run it with `-with-conda` or `-with-docker`. Your task now is to run it again `-with-docker`, but without creating your own container image. Instead, use the BioContainers image for salmon 1.7.0.
+    During the earlier RNA-Seq tutorial (script2.nf), you created an index with the salmon tool. Given you do not have salmon installed locally in the machine provided by GitHub Codespaces, you had to either run it with `-with-conda` or `-with-docker`. Your task now is to run it again `-with-docker`, but without creating your own container image. Instead, use the BioContainers image for salmon 1.7.0.
 
 
     ??? Solution

diff --git a/docs/basic_training/containers.pt.md b/docs/basic_training/containers.pt.md
@@ -2,6 +2,13 @@
 description: Material de treinamento básico do Nextflow
 ---
 
+!!! warning
+
+    Some of the translations on the training portal are out of date.
+    The translated material may be incomplete or incorrect.
+    We plan to update the translations later this year.
+    In the meantime, please try to work through the English-language material if you can.
+
 # Gerencie dependências e contêineres
 
 Fluxos de trabalhos computacionais são raramente compostos de um só script ou ferramenta. Muitas vezes, eles dependem de dúzias de componentes de softwares ou bibliotecas.
@@ -181,7 +188,7 @@ docker run --volume $PWD:$PWD --workdir $PWD minha-imagem \
 Ou definir uma pasta que você queira montar como uma variável de ambiente, chamada `DATA`:
 
 ```bash
-DATA=/workspace/gitpod/nf-training/data
+DATA=/workspaces/training/nf-training/data
 docker run --volume $DATA:$DATA --workdir $PWD minha-imagem \
     salmon index -t $PWD/data/ggal/transcriptome.fa -i transcript-index
 ```

diff --git a/docs/basic_training/debugging.fr.md b/docs/basic_training/debugging.fr.md
@@ -3,6 +3,13 @@ titre: Description
 du Dépannage: Traitement des erreurs et dépannage
 ---
 
+!!! warning
+
+    Some of the translations on the training portal are out of date.
+    The translated material may be incomplete or incorrect.
+    We plan to update the translations later this year.
+    In the meantime, please try to work through the English-language material if you can.
+
 # Traitement des erreurs et dépannage
 
 ## Débogage des erreurs d'exécution

diff --git a/docs/basic_training/debugging.pt.md b/docs/basic_training/debugging.pt.md
@@ -3,6 +3,13 @@ title: Resolução de problemas
 description: Tratamento de erros e resolução de problemas
 ---
 
+!!! warning
+
+    Some of the translations on the training portal are out of date.
+    The translated material may be incomplete or incorrect.
+    We plan to update the translations later this year.
+    In the meantime, please try to work through the English-language material if you can.
+
 # Tratamento de erros e resolução de problemas
 
 ## Depuração de erros de execução

diff --git a/docs/basic_training/executors.fr.md b/docs/basic_training/executors.fr.md
@@ -2,6 +2,13 @@
 description: Atelier de formation de base sur Nextflow
 ---
 
+!!! warning
+
+    Some of the translations on the training portal are out of date.
+    The translated material may be incomplete or incorrect.
+    We plan to update the translations later this year.
+    In the meantime, please try to work through the English-language material if you can.
+
 # Scénarios de déploiement
 
 Les applications génomiques du monde réel peuvent engendrer l'exécution de milliers de tâches. Dans ce scénario, un planificateur de lots est généralement utilisé pour déployer un workflow dans un cluster informatique, permettant l'exécution de nombreuses tâches en parallèle sur de nombreux nœuds informatiques.

diff --git a/docs/basic_training/executors.pt.md b/docs/basic_training/executors.pt.md
@@ -2,6 +2,13 @@
 description: Material de treinamento básico do Nextflow
 ---
 
+!!! warning
+
+    Some of the translations on the training portal are out of date.
+    The translated material may be incomplete or incorrect.
+    We plan to update the translations later this year.
+    In the meantime, please try to work through the English-language material if you can.
+
 # Cenários de implantação
 
 Aplicações genômicas do mundo real podem gerar milhares de tarefas sendo executadas. Nesse cenário, um escalonador de lote (batch scheduler) é comumente usado para implantar um fluxo de trabalho em um cluster de computação, permitindo a execução de muitos trabalhos em paralelo em muitos nós de computação.

diff --git a/docs/basic_training/groovy.pt.md b/docs/basic_training/groovy.pt.md
@@ -3,6 +3,13 @@ title: Introdução ao Groovy
 description: Uma introdução rápida às estruturas básicas e expressões do Groovy
 ---
 
+!!! warning
+
+    Some of the translations on the training portal are out of date.
+    The translated material may be incomplete or incorrect.
+    We plan to update the translations later this year.
+    In the meantime, please try to work through the English-language material if you can.
+
 # Estruturas básicas e expressões do Groovy
 
 Nextflow é uma linguagem específica de domínio (DSL) implementada sobre a linguagem de programação Groovy, que por sua vez é um superconjunto da linguagem de programação Java. Isso significa que o Nextflow pode executar qualquer código Groovy ou Java.

diff --git a/docs/basic_training/img/gitpod.welcome.png b/docs/basic_training/img/gitpod.welcome.png
diff --git a/docs/basic_training/index.es.md b/docs/basic_training/index.es.md
@@ -4,6 +4,13 @@ hide:
   - toc
 ---
 
+!!! warning
+
+    Some of the translations on the training portal are out of date.
+    The translated material may be incomplete or incorrect.
+    We plan to update the translations later this year.
+    In the meantime, please try to work through the English-language material if you can.
+
 # Bienvenido
 
 Nos complace acompañarlo en el camino para escribir flujos de trabajo científicos reproducibles y escalables usando Nextflow. Esta guía complementa la documentación completa de Nextflow; si alguna vez tienes alguna duda, diríjete a los documentos que se encuentran en el siguiente [enlace](https://www.nextflow.io/docs/latest).

diff --git a/docs/basic_training/index.fr.md b/docs/basic_training/index.fr.md
@@ -4,6 +4,13 @@ hide:
   - toc
 ---
 
+!!! warning
+
+    Some of the translations on the training portal are out of date.
+    The translated material may be incomplete or incorrect.
+    We plan to update the translations later this year.
+    In the meantime, please try to work through the English-language material if you can.
+
 # Bienvenue
 
 Nous sommes heureux de vous accompagner sur le chemin de rédaction de workflows scientifiques reproductibles et évolutifs en utilisant Nextflow. Ce guide complète toute la documentation de Nextflow - si vous avez des doutes, consultez la documentation située [ici](https://www.nextflow.io/docs/latest).

diff --git a/docs/basic_training/index.md b/docs/basic_training/index.md
@@ -4,7 +4,7 @@ You are now on the path to writing reproducible and scalable scientific workflow
 
 Let's get started!
 
-[![Open in Gitpod](https://img.shields.io/badge/Gitpod-%20Open%20in%20Gitpod-908a85?logo=gitpod)](https://gitpod.io/#https://github.com/nextflow-io/training)
+[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/nextflow-io/training?quickstart=1&ref=master)
 
 ## Learning objectives
 

diff --git a/docs/basic_training/index.pt.md b/docs/basic_training/index.pt.md
@@ -4,6 +4,13 @@ hide:
   - toc
 ---
 
+!!! warning
+
+    Some of the translations on the training portal are out of date.
+    The translated material may be incomplete or incorrect.
+    We plan to update the translations later this year.
+    In the meantime, please try to work through the English-language material if you can.
+
 # Bem vindo ao treinamento básico do Nextflow
 
 Estamos entusiasmados em tê-lo no caminho para escrever fluxos de trabalho científicos reprodutíveis e escaláveis usando o Nextflow. Este guia complementa a documentação oficial do Nextflow - se você tiver alguma dúvida, acesse a documentação oficial localizada [aqui](https://www.nextflow.io/docs/latest).

diff --git a/docs/basic_training/intro.fr.md b/docs/basic_training/intro.fr.md
@@ -2,6 +2,13 @@
 description: Démarrer avec Nextflow
 ---
 
+!!! warning
+
+    Some of the translations on the training portal are out of date.
+    The translated material may be incomplete or incorrect.
+    We plan to update the translations later this year.
+    In the meantime, please try to work through the English-language material if you can.
+
 # Introduction
 
 ## Concepts de base

diff --git a/docs/basic_training/intro.md b/docs/basic_training/intro.md
@@ -166,7 +166,7 @@ Now copy the above example into your favorite text editor and save it to a file
 
 !!! warning
 
-    For the Gitpod tutorial, make sure you are in the folder called `nf-training`
+    For the GitHub Codespaces tutorial, make sure you are in the folder called `nf-training`
 
 Execute the script by entering the following command in your terminal:
 

diff --git a/docs/basic_training/intro.pt.md b/docs/basic_training/intro.pt.md
@@ -2,6 +2,13 @@
 description: Introdução ao Nextflow
 ---
 
+!!! warning
+
+    Some of the translations on the training portal are out of date.
+    The translated material may be incomplete or incorrect.
+    We plan to update the translations later this year.
+    In the meantime, please try to work through the English-language material if you can.
+
 # Introdução
 
 ## Conceitos básicos

diff --git a/docs/basic_training/modules.pt.md b/docs/basic_training/modules.pt.md
@@ -2,6 +2,13 @@
 description: Material de treinamento básico do Nextflow
 ---
 
+!!! warning
+
+    Some of the translations on the training portal are out of date.
+    The translated material may be incomplete or incorrect.
+    We plan to update the translations later this year.
+    In the meantime, please try to work through the English-language material if you can.
+
 # Modularização
 
 A definição de bibliotecas modulares simplifica a escrita de fluxos de trabalho complexos de análise de dados, além tornar o reuso de processos mais fácil.