Tags: nextflow-io/training
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Fix orphaned file deletion not being included in translation PRs (#862) * Fix orphaned file deletion not being included in translation PRs The translate job deletes orphaned files but artifacts only contain new/updated translations. The merge job now runs ci-delete-orphans to delete orphans and stage them via git rm before creating the PR. * Translation: run pre-commit on all files
Update Hello Nextflow videos to 2026 versions (#856) * Update playlist link * Add new video transcripts * Remove old translated transcripts * Update Hello Nextflow videos to 2026 versions * Add cc_load_policy and cc_lang_pref params to YouTube embeds * Updated 'hello workflows' video to fixed version
Pin nf-core to 3.4.1 for training stability (#726) * Pin nf-core to 3.4.1 for training stability PR #683 enabled automatic installation of the latest nf-core version by adding Python 3.13 support. While this approach ensures access to new features, pinning to a specific version provides consistency for training environments where reproducible behavior is important. Related to #683 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]> * Fix check-headings workflow to run on all PRs The workflow was only triggered when markdown files changed, causing it to be skipped entirely for non-markdown PRs. Since check-headings is a required status check, this blocked PRs that didn't touch markdown. Now the workflow runs on all PRs but conditionally skips the actual check when no markdown files have changed. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]> --------- Co-authored-by: Claude <[email protected]>
✨ 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]>
Add Scripting essentials module (#652) * Add AI-assisted Groovy essentials * Refine section 1.1 * Add groovy essentials to nav * Fix list rendering * Emphasise departure to groovy * Shorten intro * Shorten intro * Fix highlight * Refine section 1.2 * messy updates up to section 4 * State after a good chat wiht Claude code * Tone down intro * Reset collect.nf to starting state * Tweaks * Reset collect.nf to starting state * Tweaks * Revert main.nf to starting point * Tweaks * backticks fix? * Reset fastp module to starting point * Fix fastp * tweaks * latest tweaks, simplify the variable interpretation part * Reorg subsections a bit * Fix highlights * Fix up dynamic resources * Fix up dynamic routing * Final tweaks * Language/ clarity improvements * Prettier * Apply suggestions from code review Co-authored-by: Copilot <[email protected]> * Add teach time estimate for groovy * Fix formatting * Some section 2 fixes * Fix highlights * Fix tiny issues * More Groovy fixes * update time estimate * Refactor Groovy Essentials to Essential Scripting Patterns Address reviewer feedback to reframe content away from "Nextflow vs Groovy" and toward presenting Nextflow as a standalone language. Major changes: - Renamed from groovy_essentials to essential_scripting_patterns - Updated terminology: "dataflow vs scripting" instead of "Nextflow vs Groovy" - Reframed collect example as Channel vs Iterable types in Nextflow standard library - Added historical context about Groovy while emphasizing Nextflow language specification - Updated all code comments and examples to reference Nextflow standard library - Prioritized Nextflow documentation in resources section 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]> * Prettier * Update title to Essential Nextflow Scripting Patterns 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]> * Apply suggestions from code review Co-authored-by: Ben Sherman <[email protected]> * Easy fixes for Ben * Iterable -> List * Fixes up to handlers * Fix highlight * Tighten intro * Tiny fixes --------- Co-authored-by: Copilot <[email protected]> Co-authored-by: Claude <[email protected]> Co-authored-by: Ben Sherman <[email protected]>
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