✨ feat: nextflow run for bioimaging (#680)

* devexp 💻: add live preview vscode ext for multiqc viewing

* ✨ feat(training): add Nextflow for Bioimaging course

Add comprehensive training course for running nf-core/molkart pipeline
and spatial transcriptomics bioimaging workflows. Includes:

- Course documentation with orientation, basics, and molkart execution
- Input configuration and parameter customization guides
- Example workflows (hello-world.nf) and sample data
- Integration into nf4_science training collection

This course teaches users how to run bioimaging pipelines using the
Nextflow Run pattern with nf-core/molkart as the primary example.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>

* 📝 docs(imaging): complete Nextflow run for Imaging course content

Complete the imaging course documentation with comprehensive coverage of running nf-core/molkart pipeline including inputs and configuration.

- Streamline orientation page, remove redundant content
- Add molkart pipeline diagram (img/molkart.png)
- Improve Part 2 with clearer explanations and output examples
- Complete Part 3 with parameter files and samplesheet examples
- Complete Part 4 with configuration profiles and resource management
- Update course title to "Nextflow run for Imaging"
- Add Parts 3 and 4 to navigation in mkdocs.yml

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>

* 📝 docs(imaging): apply suggestions from code review
                                                                        │
Update imaging course documentation with improved clarity and consistency:
    - Clarify file content descriptions in basics module
    - Add cross-reference to Hello nf-core course
    - Update command examples to use tree instead of ls
    - Enhance explanations of nf-core conventions and resume functionality
    - Improve configuration section clarity on profiles and process labels
    - Remove training subset section to streamline course flow

Co-Authored-By: ashdederich <[email protected]>
Co-Authored-By: pinin4fjords <[email protected]>

* 📝 docs(imaging): cleanup content prior to release

* 📑 docs (imaging): apply suggestions from code review

Co-authored by: Florian Wuennemann <[email protected]>

* 📊 survey: add survey link for imaging course

---------

Co-authored-by: Claude <[email protected]>
Co-authored-by: ashdederich <[email protected]>
Co-authored-by: pinin4fjords <[email protected]>
Co-authored-by: Florian Wuennemann <[email protected]>

Author: 5 people

.devcontainer/codespaces-dev/devcontainer.json

@@ -40,7 +40,10 @@
     "onCreateCommand": "bash .devcontainer/setup.sh",
     "customizations": {
         "vscode": {
-            "extensions": ["nf-core.nf-core-extensionpack"],
+            "extensions": [
+                "nf-core.nf-core-extensionpack",
+                "ms-vscode.live-server"
+            ],
             // Use Python from conda
             "settings": {
                 "python.defaultInterpreterPath": "/opt/conda/bin/python"

.devcontainer/devcontainer.json

@@ -20,7 +20,10 @@
     "onCreateCommand": "bash .devcontainer/setup.sh",
     "customizations": {
         "vscode": {
-            "extensions": ["nf-core.nf-core-extensionpack"],
+            "extensions": [
+                "nf-core.nf-core-extensionpack",
+                "ms-vscode.live-server"
+            ],
             // Use Python from conda
             "settings": {
                 "python.defaultInterpreterPath": "/opt/conda/bin/python"

.devcontainer/local-dev/devcontainer.json

@@ -42,7 +42,10 @@
     "postCreateCommand": "mkdir -p /workspaces && rm -rf /workspaces/training && ln -s ${localWorkspaceFolder} /workspaces/training",
     "customizations": {
         "vscode": {
-            "extensions": ["nf-core.nf-core-extensionpack"],
+            "extensions": [
+                "nf-core.nf-core-extensionpack",
+                "ms-vscode.live-server"
+            ],
             // Use Python from conda
             "settings": {
                 "python.defaultInterpreterPath": "/opt/conda/bin/python",

docs/index.md

@@ -100,6 +100,16 @@ These are courses that demonstrate how to apply the concepts and components pres
 
     [Start the Nextflow for RNAseq training :material-arrow-right:](nf4_science/rnaseq/){ .md-button .md-button--primary }
 
+!!! exercise "Nextflow for Imaging"
+
+    !!! tip inline end ""
+
+        :material-microscope:{.nextflow-primary} Learn to run pipelines for spatial transcriptomics imaging data in Nextflow.
+
+    This is a course for researchers in imaging and spatial omics who wish to learn how to run and customize analysis pipelines. The course uses the nf-core/molkart pipeline to provide a biologically-relevant pipeline demonstrate how to run, configure, and manage inputs for Nextflow pipelines workflows.
+
+    [Start the Nextflow for Imaging training :material-arrow-right:](nf4_science/imaging/){ .md-button .md-button--primary }
+
 Let us know what other domains and use cases you'd like to see covered here by posting in the [Training section](https://community.seqera.io/c/training/) of the community forum.
 
 ## Advanced Nextflow Training

docs/nf4_science/imaging/00_orientation.md

@@ -0,0 +1,53 @@
+# Orientation
+
+This orientation assumes you have already opened the training environment by clicking on the "Open in GitHub Codespaces" button.
+If not, please do so now, ideally in a second browser window or tab so you can refer back to these instructions.
+
+[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new?hide_repo_select=true&ref=master&repo=290790519&skip_quickstart=true&machine=premiumLinux&devcontainer_path=.devcontainer%2Fdevcontainer.json)
+
+!!!warning "Machine size requirement"
+
+    Make sure to select an **8-core machine** when creating your Codespace for this training course. The bioimaging workflows require additional compute resources.
+
+## GitHub Codespaces
+
+The GitHub Codespaces environment contains all the software, code and data necessary to work through this training course, so you don't need to install anything yourself.
+However, you do need a (free) GitHub account to log in, and if you are unfamiliar with the interface you should take a few minutes to familiarize yourself with it by completing the [GitHub Codespaces Orientation](../../envsetup/index.md) mini-course.
+
+## Pre-download Docker images
+
+Once you've opened your Codespace, let's pre-download all the Docker images we'll need for this training course.
+This will save time later and ensure smooth execution of the workflows.
+
+Open a new terminal tab and run the following command:
+
+```bash
+nextflow run nf-core/molkart -profile docker,test -stub -resume --outdir results
+```
+
+This command will download all necessary Docker images in the background.
+You can continue with the rest of the orientation while this runs.
+
+!!!tip
+
+    The `-stub` flag allows the pipeline to run quickly without processing real data, which is perfect for downloading images. You can monitor the progress in the terminal tab.
+
+## Working directory
+
+Throughout this training course, we'll be working in the `nf4-science/imaging/` directory.
+
+Change directory now by running this command in the terminal:
+
+```bash
+cd nf4-science/imaging/
+```
+
+!!!tip
+
+    If for whatever reason you move out of this directory, you can always use the full path to return to it, assuming you're running this within the GitHub Codespaces training environment:
+
+    ```bash
+    cd /workspaces/training/nf4-science/imaging
+    ```
+
+**Now, to begin the course, click on the arrow in the bottom right corner of this page.**