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CLAUDE.md

This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.

Project Overview

This tool monitors nf-core Nextflow pipelines, modules, and subworkflows for strict syntax linting errors. It clones repositories, runs nextflow lint, and generates health reports with trend charts.

Commands

# Install dependencies
pip install -e .

# Run the linter on all nf-core pipelines, modules, and subworkflows
strict-syntax-health

# Update the pipelines list from nf-co.re before running
strict-syntax-health --update-pipelines

# Update README.md with results
strict-syntax-health --update-readme

# Lint specific pipeline(s) only
strict-syntax-health -p demo -p rnaseq

# Lint specific module(s) or subworkflow(s)
strict-syntax-health -m bwa_mem -m samtools_sort
strict-syntax-health -s bam_sort_stats_samtools

# Skip specific types
strict-syntax-health --skip-modules --skip-subworkflows  # Only lint pipelines
strict-syntax-health --skip-pipelines                     # Only lint modules/subworkflows

# Regenerate charts/README from existing results (no linting)
strict-syntax-health --generate-charts-only --update-readme

# Ignore cache and re-lint everything
strict-syntax-health --no-cache

# Run pre-commit hooks (uses prek instead of pre-commit)
prek run --all-files

Architecture

Single-module CLI (src/strict_syntax_health/cli.py) using rich-click:

  1. Pipeline discovery: Fetches pipelines.json from nf-co.re, filters out archived pipelines
  2. Module/Subworkflow discovery: Clones nf-core/modules repo, discovers components from directory structure
  3. Cloning: Shallow clones pipelines to pipelines/ directory, nf-core/modules to modules/
  4. Linting: Runs nextflow lint on each component, parses JSON output
  5. History tracking: Stores daily aggregates in lint_results/history.json (counts by error/warning severity buckets)
  6. Chart generation: Creates stacked area charts with Plotly showing trends over time
  7. README generation: Outputs markdown with charts and collapsible result tables for each type

Directory Structure

pipelines/
├── pipelines.json          # Pipeline list from nf-co.re (tracked in git)
└── <cloned pipeline repos> # (gitignored)

modules/                    # nf-core/modules clone (gitignored)

lint_results/
├── history.json            # Combined history for pipelines, modules, subworkflows
├── pipelines/
│   ├── errors_chart.png
│   ├── warnings_chart.png
│   └── <pipeline>_lint.md
├── modules/
│   ├── errors_chart.png
│   ├── warnings_chart.png
│   └── <module>_lint.md
└── subworkflows/
    ├── errors_chart.png
    ├── warnings_chart.png
    └── <subworkflow>_lint.md

External Dependencies

  • Nextflow: Must be installed and available on PATH. In CI, it's built from the master branch to get latest lint features.
  • Git: Required for cloning pipelines and nf-core/modules

Caching

The tool uses commit-based caching to skip unchanged repositories:

  • Pipeline results are cached by git commit hash; unchanged pipelines are skipped
  • Module/subworkflow results share a single cache keyed to the nf-core/modules repo commit
  • Use --no-cache to force re-linting everything

Code Style

  • Line length: 120 characters
  • Ruff for linting (E, F, I, W rules) and formatting
  • Double quotes for strings