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 <noreply@anthropic.com>
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 <noreply@anthropic.com>
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 <noreply@anthropic.com>
- 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 <noreply@anthropic.com>
- 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 <noreply@anthropic.com>
- 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 <noreply@anthropic.com>
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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 <noreply@anthropic.com>
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 <noreply@anthropic.com>
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 <noreply@anthropic.com>
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 <noreply@anthropic.com>
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 <noreply@anthropic.com>
Changed from numbered list to bold headings with bullet lists to prevent all items from rendering as a single 10-item numbered list. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
Removed repetitive statement about early failure that was already established in the "Why validation matters" section above. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
Emphasized that nf-schema is a standalone Nextflow plugin that can be used in any pipeline, while also noting its heavy integration with and adoption by nf-core. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
Replaced manual JSON editing instructions with the interactive nf-core pipelines schema build workflow. Added screenshots showing the web interface for adding parameters. Emphasized that manual editing is error-prone and the GUI tool is the recommended approach. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
Changed image paths from ./img/hello_nf-core/ to ./img/ to match the convention used in other hello_nf-core lessons. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
Replaced incorrect --validationSchemaIgnoreParams command-line flag with proper nextflow.config validation block configuration. Added before/after code blocks showing how to temporarily ignore input validation during section 2 and re-enable it in section 3 after configuring the input data schema. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
Changed section 3.3 to use before/after tabs showing the transition from the template's default paired-end sequencing schema to the simpler greetings schema. This helps users understand what they're changing and why. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
Changed file path from markdown link to backticks to match repository conventions. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
Moved validation configuration content from the oddly-placed section 3.5
note to a new section 1.4 that explains how nf-schema is installed and
configured in nf-core pipelines. This section now includes:
- Explanation of how nf-schema is pre-installed in the template
- The validation{} configuration block
- The before/after edit to add ignoreParams for input validation
- Context for why we temporarily disable input file validation
Removed the duplicate content from section 2.3 (now 2.3 is just testing).
This provides better flow: users configure validation upfront in section 1,
then work through parameter validation in section 2, and finally re-enable
input validation in section 3.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
- Fixed test command to use 'nextflow run .' consistently - Fixed cross-reference from section 3.6 (was 2.3, should be 1.4) - Improved clarity of verification step with bold header - Updated test output examples to be more accurate 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
Added a "What does the Hello Nextflow workflow do?" subsection at the start of section 2 to provide context for users who may not have completed the Hello Nextflow training course. This explains the workflow's purpose and functionality before diving into making it composable. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
Added "What you'll learn" section to orientation that explains the five core concepts covered in the course and why they matter. Sets expectations that we can't be exhaustive but focus on essential concepts for getting started with nf-core. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
Created a new summary page that wraps up the course by: - Highlighting what learners built (the core-hello pipeline) - Summarizing the five key skills acquired - Explaining the transformation from research script to production pipeline This provides closure before the survey and next steps pages. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
Replaced the large Congratulations section with a simple "What's next?" that directs users to the new summary page. This avoids duplication and maintains consistent flow across all parts that end with "What's next?". 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
Remove trailing whitespace from cowpy module files to pass editorconfig checks. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
- Remove trailing whitespace from snap files - Add newlines at end of snap files - Remove extra blank line from utils_nfschema_plugin/main.nf 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
pinin4fjords
changed the title
vdauwera
changed the title
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I took the liberty of updating your PR's name since the scope has significantly expanded since you started it, and it will make more sense later if the PR is referenced. |
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 <noreply@anthropic.com>
…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 <noreply@anthropic.com>
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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