Nextflow to TOPP workflow conversion guide #304
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Comprehensive documentation for converting nf-core/Nextflow workflows that use OpenMS TOPP tools to the Streamlit-based TOPP Workflow Framework. Includes: - Step-by-step conversion methodology - Channel-to-FileManager mapping patterns - Parameter schema conversion - Common patterns (parallel, collection, grouping, conditionals) - Complete example workflow conversion - Reference tables for Nextflow-to-TOPP mappings
📝 WalkthroughWalkthroughTwo documentation files have been added to guide users in converting Nextflow workflows to the TOPP Workflow Framework. A subsection was added to Changes
Estimated code review effort🎯 2 (Simple) | ⏱️ ~15 minutes Poem
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Actionable comments posted: 1
🤖 Fix all issues with AI agents
In `@docs/nextflow_conversion_guide.md`:
- Line 1187: The markdown link "[TOPP Workflow Framework Documentation]"
currently points to "../content/topp_workflow_docs.py" which doesn't exist;
update that link to point to an existing file (for example change the target to
"../content/documentation.py") or replace the link with a note that this is
app-internal documentation (e.g., "TOPP Workflow Framework Documentation
(app-internal)") so the README no longer references a missing file; edit the
line containing the link text and target to correct the path or clarify its
status.
🧹 Nitpick comments (4)
docs/nextflow_conversion_guide.md (4)
69-76: Add language specifier to fenced code block.The table in this code block should have a language specifier for proper rendering and syntax highlighting. Consider using
textormarkdownas the language identifier.📝 Proposed fix
-``` +```text Process Name | TOPP Tool | Inputs | Outputs | Key Parameters -------------|-----------|--------|---------|--------------- DECOYDATABASE | DecoyDatabase | fasta | fasta | decoy_stringBased on static analysis hints.
82-101: Add language specifier to fenced code block.The ASCII diagram should have a language specifier. Consider using
textfor plain text diagrams.📝 Proposed fix
-``` +```text Input Files │ ▼Based on static analysis hints.
158-165: Add language specifier to fenced code block.This parameter mapping table should have a language specifier for consistency with other code blocks in the document.
📝 Proposed fix
-``` +```text Nextflow Param | TOPP Tool | TOPP Parameter | UI Widget ----------------------|----------------|--------------------------|----------Based on static analysis hints.
1159-1183: Use proper heading tags instead of bold text.In the troubleshooting section, the issue titles (e.g., "1. Tool not found") should use proper Markdown heading syntax (e.g.,
####) instead of bold text for better document structure and accessibility.📝 Proposed fix
-**1. Tool not found** -``` +#### 1. Tool not found + +```text ERROR: FeatureFinderMetabo: command not found-2. File not found errors
-+#### 2. File not found errors + +text
ERROR: Input file does not exist: /path/to/file.mzML-**3. Parameter not applied** -``` +#### 3. Parameter not applied + +```text Parameter noise_threshold not being used-4. Parallel execution issues
-+#### 4. Parallel execution issues + +text
Only one file processed instead of allBased on static analysis hints.
📜 Review details
Configuration used: Organization UI
Review profile: CHILL
Plan: Pro
📒 Files selected for processing (2)
docs/build_app.mddocs/nextflow_conversion_guide.md
🧰 Additional context used
🪛 markdownlint-cli2 (0.18.1)
docs/nextflow_conversion_guide.md
69-69: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
82-82: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
158-158: Fenced code blocks should have a language specified
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1159-1159: Emphasis used instead of a heading
(MD036, no-emphasis-as-heading)
1160-1160: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
1165-1165: Emphasis used instead of a heading
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1166-1166: Fenced code blocks should have a language specified
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1171-1171: Emphasis used instead of a heading
(MD036, no-emphasis-as-heading)
1172-1172: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
1177-1177: Emphasis used instead of a heading
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1178-1178: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
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- GitHub Check: build-full-app
- GitHub Check: build-openms
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🔇 Additional comments (1)
docs/build_app.md (1)
70-78: LGTM! Clear and well-integrated documentation addition.The new subsection effectively introduces Nextflow workflow conversion and provides a helpful summary of what the linked guide covers. The integration with the existing "Complex workflow using TOPP tools" section is logical and well-placed.
✏️ Tip: You can disable this entire section by setting review_details to false in your review settings.
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| ## Additional Resources | ||
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| - [TOPP Workflow Framework Documentation](../content/topp_workflow_docs.py) - Interactive docs in the app |
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🧩 Analysis chain
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Fix the broken documentation link.
The referenced file topp_workflow_docs.py does not exist in the content/ directory. Either create this file, update the link to reference an existing file (e.g., documentation.py), or clarify that this is app-internal documentation that doesn't correspond to a repository file.
🤖 Prompt for AI Agents
In `@docs/nextflow_conversion_guide.md` at line 1187, The markdown link "[TOPP
Workflow Framework Documentation]" currently points to
"../content/topp_workflow_docs.py" which doesn't exist; update that link to
point to an existing file (for example change the target to
"../content/documentation.py") or replace the link with a note that this is
app-internal documentation (e.g., "TOPP Workflow Framework Documentation
(app-internal)") so the README no longer references a missing file; edit the
line containing the link text and target to correct the path or clarify its
status.
Comprehensive documentation for converting nf-core/Nextflow workflows that use OpenMS TOPP tools to the Streamlit-based TOPP Workflow Framework.
Includes:
Summary by CodeRabbit
✏️ Tip: You can customize this high-level summary in your review settings.