Merge branch 'master' into tools-update

Author: mribeirodantas

.devcontainer/devcontainer.json

@@ -1,27 +1,30 @@
 {
     "name": "nfcore",
-    "image": "nfcore/gitpod:latest",
+    "image": "ghcr.io/nextflow-io/training:latest",
     "remoteUser": "gitpod",
-
+    "features": {
+        "ghcr.io/devcontainers/features/docker-outside-of-docker:1": {}
+    },
+    "remoteEnv": {
+        "NXF_HOME": "/workspaces/.nextflow",
+        "HOST_PROJECT_PATH": "${localWorkspaceFolder}"
+    },
     // Configure tool-specific properties.
     "customizations": {
         // Configure properties specific to VS Code.
         "vscode": {
             // Set *default* container specific settings.json values on container create.
             "settings": {
-                "python.defaultInterpreterPath": "/opt/conda/bin/python",
-                "python.linting.enabled": true,
-                "python.linting.pylintEnabled": true,
-                "python.formatting.autopep8Path": "/opt/conda/bin/autopep8",
-                "python.formatting.yapfPath": "/opt/conda/bin/yapf",
-                "python.linting.flake8Path": "/opt/conda/bin/flake8",
-                "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
-                "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
-                "python.linting.pylintPath": "/opt/conda/bin/pylint"
+                "python.defaultInterpreterPath": "/opt/conda/bin/python"
             },
-
             // Add the IDs of extensions you want installed when the container is created.
-            "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
+            "extensions": [
+                "ms-python.python",
+                "ms-python.vscode-pylance",
+                "nf-core.nf-core-extensionpack",
+                "nextflow.nextflow",
+                "codezombiech.gitignore"
+            ]
         }
     },
     "portsAttributes": {

.github/gitpod.Dockerfile

@@ -15,14 +15,17 @@ RUN apt-get update --quiet && \
         curl \
         tree \
         graphviz \
-        software-properties-common
-
+        software-properties-common && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
 
 # Taken from: https://github.com/nf-core/tools/blob/master/nf_core/gitpod/gitpod.Dockerfile
 # Install Apptainer (Singularity)
 RUN add-apt-repository -y ppa:apptainer/ppa && \
     apt-get update --quiet && \
-    apt install -y apptainer
+    apt install -y apptainer && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
 
 # Install Conda
 RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
@@ -35,6 +38,11 @@ ENV PATH="/opt/conda/bin:$PATH"
 RUN mkdir -p /workspace/data \
     && chown -R gitpod:gitpod /opt/conda /workspace/data
 
+# Install Tower Agent
+RUN curl -fSL https://github.com/seqeralabs/tower-agent/releases/latest/download/tw-agent-linux-x86_64 > tw-agent && \
+    chmod +x tw-agent && \
+    mv tw-agent /usr/local/bin/tw-agent
+
 # Change user to gitpod
 USER gitpod
 

.gitpod.yml

@@ -23,14 +23,14 @@ tasks:
     - before: printf 'unset JAVA_TOOL_OPTIONS\n' >> $HOME/.bashrc && exit
 
     - name: Start web server
-      command: gp ports await 23000 && gp preview https://training.nextflow.io
+      command: gp ports await 23000 && gp preview https://training.nextflow.io/hello_nextflow
 
     - name: Load Nextflow Tutorial
       command: docker pull -q nextflow/rnaseq-nf
 
     - name: Start Nextflow Tutorial
       command: |
-          cd nf-training
+          cd hello-nextflow
           source $HOME/.bashrc
           export PS1='\[\e[3;36m\]${PWD/*\//} ->\[\e[0m\] '
           unset JAVA_TOOL_OPTIONS

.pre-commit-config.yaml

@@ -11,3 +11,13 @@ repos:
       hooks:
           - id: editorconfig-checker
             alias: ec
+
+    - repo: https://github.com/pre-commit/pre-commit-hooks
+      rev: v5.0.0
+      hooks:
+          - id: trailing-whitespace
+            exclude_types:
+                - svg
+          - id: end-of-file-fixer
+            exclude_types:
+                - svg

README.md

@@ -9,20 +9,20 @@ We are excited to have you on the path to writing reproducible and scalable scie
 
 -   👉🏻 Written training material: <https://training.nextflow.io>
 
--   👩🏻‍💻 Instructions on loading this repository within a GitPod environment: <https://training.nextflow.io/basic_training/setup/>
+-   👩🏻‍💻 Instructions on loading this repository within a GitPod environment: <https://training.nextflow.io/envsetup/>
 
 -   📚 Nextflow documentation: <https://www.nextflow.io/docs/latest/>
 
 ## Contributions
 
-We welcome fixes and improvements from the community. Please fork the repository and create pull-requests with any improvements to the docs.
+We welcome fixes and improvements from the community. Please fork the repository and create pull-requests with any improvements you'd like to suggest to the docs.
 
 You can find instructions about how to develop the training material code in [`CONTRIBUTING.md`](CONTRIBUTING.md). If you want to contribute with a translation instead, check [`TRANSLATING.md`](TRANSLATING.md).
 
 ## Credits & Copyright
 
-All training material was originally written by [Seqera](https://seqera.io) but has been made open-source ([CC BY-NC-ND](https://creativecommons.org/licenses/by-nc-nd/4.0/)) for the community.
+This training material is developed and maintained by [Seqera](https://seqera.io) and released under an open-source license ([CC BY-NC-ND](https://creativecommons.org/licenses/by-nc-nd/4.0/)) for the benefit of the community. You are welcome to reuse these materials according to the terms of the license. If you are an instructor running your own trainings, we'd love to hear about how it goes and what we could do to make it easier.
 
 <a rel="license" href="http://creativecommons.org/licenses/by-nc-nd/4.0/"><img alt="Creative Commons License" src="docs/assets/img/cc_by-nc-nd.svg" /></a>
 
-> Copyright 2020-2023, Seqera. All examples and descriptions are licensed under the <a rel="license" href="http://creativecommons.org/licenses/by-nc-nd/4.0/">Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License</a>.
+> Copyright 2024, Seqera. All examples and descriptions are licensed under the <a rel="license" href="http://creativecommons.org/licenses/by-nc-nd/4.0/">Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License</a>.

docs/advanced/index.md

@@ -1,4 +1,4 @@
-# Introduction
+# Advanced Training
 
 Welcome to our Nextflow workshop for intermediate and advanced users!