Merge pull request #507 from ewels/codespaces-2.1

Cherry-pick to master: Goodbye GitPod, hello GitHub Codespaces

Author: ewels

.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

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/>
 

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
 

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
 

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
 }
 ```

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.

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.

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

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:

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.