Polish and enhance Hello nf-core training materials #691
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The previous text suggested learners could infer required parameters by examining what was present/absent in the test profile config. This is misleading - the test profile only shows pre-configured values, not requirements. Changed section 2.1 to: - Emphasize what the test profile *provides* (pre-configured input) - Point to the usage example comment as the source for --outdir info - Avoid suggesting we can infer requirements from config structure This keeps the pedagogical value while being accurate about where information comes from, deferring proper param discovery (via schema) to later sections. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
Standardized all Nextflow version references in the Hello nf-core training materials to version 25.04.3. Updated files: - 01_run_demo.md: 24.10.0 → 25.04.3 - 02_rewrite_hello.md: 24.10.4 → 25.04.3 (4 occurrences) Files 03_use_module.md and 05_input_validation.md already had the correct version. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
Updated all references to nf-core/demo from version 1.0.1 to 1.0.2 to reflect the current release. Changes: - Console output example showing pipeline version - Documentation link to nf-co.re/demo 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
- Fix typo: 'Netxflow' → 'Nextflow' - Remove duplicate line in tree output - Consolidate WoW side quest references (remove redundant mention) - Add explanation of container profiles before first use - Standardize cross-reference paths to use relative URLs 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
- Standardize terminology: use 'pipeline documentation page' consistently - Improve voice consistency: prefer inclusive 'we' over imperative - Reduce passive voice: make Nextflow the active subject - Fix grammar: 'specifics of what' and 'retrieve pipelines' 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
- Add note about variable console output (timestamps, paths, names) - Add transition paragraph between user and developer perspectives - Clarify focus on file hierarchy vs code syntax These improvements help set learner expectations and smooth pedagogical flow. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
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Priority fixes: - Fix grammar: 'inputs are handle' → 'inputs are handled' - Fix directory typo: 'config' → 'conf' - Remove incorrect line number reference - Remove redundant WoW side quest reference (already mentioned earlier) - Standardize WoW reference format to match Part 1 Style improvements: - Add transitional text between sections 3 and 4 - Add motivation for dummy entrypoint workflow in section 2.6 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
Section 3 was confusing because: - No clear transition from testing composable workflow back to nf-core scaffold - Ambiguous references to "original workflow" without specifying source/destination Improvements: - Add explicit transition at section 3 start explaining return to scaffold - Clarify we're integrating work from section 2 - Make FROM/TO direction clear in section 3.1 (original-hello → core-hello) - Specify directory paths explicitly to reduce ambiguity 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
Move ch_versions initialization before workflow logic rather than after. This reflects the correct pattern where: 1. Initialize empty versions channel 2. Run workflow processes (which would emit versions in real pipeline) 3. Collate versions at the end Add explanation that this ordering allows processes to mix their version outputs into ch_versions as the workflow runs, which is the intended pattern even though we're not implementing version capture yet. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
Make explicit that when copying workflow logic to nf-core scaffold, learners should: - Omit the `main:` keyword (already present) - Remove the `.view` line (console output not needed in scaffold) Update the "After" code block to show the workflow without the .view line, matching the instruction. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
The transition paragraph and first line of section 4 were saying the same thing. Consolidated into single transition paragraph that flows directly into section heading and first subsection. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
Corrected the Hello Nextflow workflow description: - sayHello writes greetings to files (doesn't add "world!") - convertToUpper operates on the greeting text - Added process names for clarity 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
…core Convert all instances of step labels and bold text pseudo-headings to proper numbered headings for consistency and better navigation. Changes: - 03_use_module.md: Convert 5 "Step X:" labels to numbered headings (1.9.1-1.9.5) - 04_make_module.md: Number 15 subsection headings (1.2.1-1.2.6, 1.3.1-1.3.4, 2.1.1-2.1.2, 2.2.1-2.2.3) - 05_input_validation.md: Convert 3 bold labels to numbered headings (2.2.1, 3.7.1-3.7.2) and fix incorrectly numbered intro sections Benefits: - Consistent numbered heading structure throughout documentation - All subsections appear in table of contents and sidebar navigation - Sections can be directly linked with anchor links - Easier to maintain with automated heading validation 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
vdauwera
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Nov 3, 2025
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Reviewed Parts 1-4 and the start of 5. I have a number of suggestions for clarifying and rearranging some bits. Happy to implement myself but it would be good to have you go over my comments first to see if there's anything you object to in principle, @pinin4fjords .
This commit addresses the straightforward editorial feedback from Geraldine's review of PR #691, focusing on improving clarity and messaging for the research pipeline audience. Changes: - Strip em-dashes throughout (replace with periods/separate sentences) - Revise messaging to avoid implying production vs research dichotomy - Remove "production-ready" claims about the toy example - Improve explanations of workflow summaries and technical concepts - Clarify ext.args benefits (avoiding many optional input parameters) - Replace jargon (e.g., "test harness") with simpler terms - Make "learn by doing" messaging more specific and actionable 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
Strip all remaining em-dashes from the hello nf-core documentation, replacing them with periods, commas, or colons as appropriate for cleaner, more straightforward technical writing. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
- Add link to Hello Nextflow configuration section in 01_run_demo.md - Rewrite workflow summary in 02_rewrite_hello.md to be more natural - Remove redundant sentence about nf-core tooling in 04_make_module.md - Restructure ext.args section with high-level overview first - Improve ext.args explanation to be more specific about what it is - Separate ext.args and publishDir discussions for better flow 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
Reorganize section 1.2.2 to present benefits first, then move the default publishDir configuration details into a note box with a link to nf-core documentation. This improves readability and flow. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
Expand the note box to explain the three parts of the default publishDir configuration: path (with workflow hierarchy explanation), mode, and saveAs. Acknowledge the complexity upfront and provide concrete example of SAMTOOLS_SORT -> samtools/. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
- Change "understand" to "learned" for better flow - Replace "boilerplate" with clearer "extra code" - Expand resource label explanation to introduce the concept 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
Addresses PR feedback about confusion around which parts of the generated module template need customization vs work as-is. Changes: - Split features in section 2.1.1 into "work as-is" vs "placeholders to customize" - Added three new sections (2.1.3-2.1.5) with before/after examples showing how to: - Define inputs and outputs for the specific tool - Write the script block with actual tool command - Implement the stub block to match script outputs - Referenced manual module work from section 1 for consistency - Clarified that features like tag, label, and when block are already functional 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
Addresses PR feedback about section structure and overconfident language. Changes: - Moved intro material (sections 1.1-1.3) to top-level overview before numbered sections - Moved configuration step (old 1.4) into section 1 as first practical step before examining schema - Renumbered all sections (old section 2 → 1, old section 3 → 2) - Updated takeaways to be less presumptuous: "You've learned" instead of "You now know", "seen in action" instead of "know how" - Removed abrupt section ending - section 1 now flows naturally from config to schema examination to adding parameters The structure now feels more complete with each section having clear practical outcomes rather than ending on pure exposition. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
The previous description "Control colored output" was vague. Changed to "Disable colored output in validation messages when set to true" to be more specific about what the parameter does. Addresses PR feedback about vague wording. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
Addresses two PR feedback items: 1. Clarified that input data validation is for sample sheet/manifest structure, NOT for validating contents of large data files (BAM, FASTQ, etc.). Added note explaining that data file validation should happen in processes on worker nodes for large-scale genomics. 2. Made monochromeLogs description more specific: "Disable colored output in validation messages when set to true" instead of vague "Control colored output" 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
Changed "Centralized configuration" to "Centralized publishing via publishDir configured in modules.config rather than hardcoded in modules" to be explicit about what this pattern covers. Addresses PR feedback that the connection wasn't clear. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
Changed testing section to check visual output first (faster and more natural for workshops), with command file inspection as an optional follow-up for those who want to see implementation details. Addresses PR feedback about making workshop experience more efficient. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
Changed "Use nf-core tooling to create modules" to "Generate modules with nf-core tools" to avoid confusion between pipeline templates and module templates. Addresses: #691 (comment) 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
If we like this new version we can implement it for all the course orientation pages that apply
plus a formatting fix to Part 1
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Polish and enhance Hello nf-core training materials
This PR significantly improves the Hello nf-core training course with comprehensive updates across all five parts, focusing on clarity, accuracy, consistency, and completeness.
We also remove the old nf-core side-quest to avoid confusion.
Major Changes
New Content
00_orientation.md) explaining the five core concepts covered and why they matter, setting expectations that the course focuses on essential concepts rather than being exhaustivesummary.md) to wrap up the course by highlighting what learners built, key skills acquired, and the transformation from research script to production pipelinePart 1: Run an nf-core pipeline (
01_run_demo.md)Part 2: Rewrite Hello for nf-core (
02_rewrite_hello.md)Part 3: Use an nf-core module (
03_use_module.md)Part 4: Make an nf-core module (
04_make_module.md)04_adapt_module.mdto better reflect the content (creating your own module)--empty-templateflag for cleaner examplesext.argsusage and flexibilityPart 5: Input validation (
05_input_validation.md)validation{}config block approachnf-core pipelines schema buildtool instead of manual JSON editingschema_input.jsonchangesnextflow run .instead ofnextflow run core-hello)Minor Improvements
Documentation Quality
Testing