From 5c7eda509d8f749a6ba1d5db895b6bb1f16e7cff Mon Sep 17 00:00:00 2001 From: Claude Date: Sun, 14 Dec 2025 17:27:34 +0000 Subject: [PATCH 1/9] refactor: update plugin to follow Python best practices - Modernize pyproject.toml with full project configuration - Add build-system specification - Configure ruff for linting and formatting - Add mypy configuration - Bump Python requirement to >=3.9 - Add pre-commit configuration - Include ruff-format and ruff-lint hooks - Add prettier for markdown/yaml formatting - Include standard hooks (trailing whitespace, merge conflict, etc.) - Add GitHub Actions linting workflow - Separate lint.yaml for ruff and prettier checks - Update linux.yaml with modern action versions and Python 3.9-3.12 - Refactor Python code - Add comprehensive type hints throughout - Use f-strings consistently - Replace deprecated pkg_resources with importlib.metadata - Remove OrderedDict (use dict in Python 3.7+) - Use contextlib.suppress instead of try-except-pass - Improve docstrings and code organization - Add CLAUDE.md for AI assistant guidance - Simplify setup.py to minimal pyproject.toml wrapper --- .github/workflows/lint.yaml | 52 +++++ .github/workflows/linux.yaml | 37 +-- .pre-commit-config.yaml | 51 +++++ .prettierignore | 30 +++ .prettierrc.js | 10 + CLAUDE.md | 131 +++++++++++ multiqc_sav/modules/sav.py | 427 ++++++++++++++++++----------------- multiqc_sav/multiqc_sav.py | 26 ++- pyproject.toml | 100 +++++++- setup.py | 44 +--- 10 files changed, 628 insertions(+), 280 deletions(-) create mode 100644 .github/workflows/lint.yaml create mode 100644 .pre-commit-config.yaml create mode 100644 .prettierignore create mode 100644 .prettierrc.js create mode 100644 CLAUDE.md diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml new file mode 100644 index 0000000..0df3ac6 --- /dev/null +++ b/.github/workflows/lint.yaml @@ -0,0 +1,52 @@ +name: "Lint" + +on: + push: + branches: [main, master] + pull_request: + +jobs: + lint: + name: Lint + runs-on: ubuntu-latest + timeout-minutes: 5 + + steps: + - name: Checkout code + uses: actions/checkout@v4 + + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version: "3.11" + + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install ruff + + - name: Ruff format check + run: ruff format --check . + + - name: Ruff lint check + run: ruff check . + + prettier: + name: Prettier + runs-on: ubuntu-latest + timeout-minutes: 5 + + steps: + - name: Checkout code + uses: actions/checkout@v4 + + - name: Set up Node.js + uses: actions/setup-node@v4 + with: + node-version: "20" + + - name: Install Prettier + run: npm install -g prettier@3.1.0 + + - name: Run Prettier check + run: prettier --check "**/*.{md,yaml,yml,json,html}" --ignore-path .prettierignore diff --git a/.github/workflows/linux.yaml b/.github/workflows/linux.yaml index b282077..0c1a36f 100644 --- a/.github/workflows/linux.yaml +++ b/.github/workflows/linux.yaml @@ -1,43 +1,48 @@ name: "Build - Linux" -on: [push, pull_request] + +on: + push: + branches: [main, master] + pull_request: jobs: - run_multiqc: + test: name: Linux - Python ${{ matrix.python-version }} runs-on: ubuntu-latest strategy: + fail-fast: false matrix: - python-version: [3.6, 3.7, 3.8, 3.9] + python-version: ["3.9", "3.10", "3.11", "3.12"] timeout-minutes: 10 steps: - # Check out MultiQC code - - uses: actions/checkout@v2 + - name: Checkout code + uses: actions/checkout@v4 - # Set up Python - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v1 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - # Update pip and install beautifulsoup4 for CI tests (CSP checking) - - name: Install dependencies for CI tests + - name: Install dependencies run: | - python -m pip install --upgrade pip setuptools beautifulsoup4 multiqc + python -m pip install --upgrade pip setuptools wheel + pip install beautifulsoup4 multiqc - # Install MultiQC - name: Install MultiQC_SAV run: pip install . - # Run all of the tests! - - name: MiSeq + - name: Test MiSeq run: multiqc -m SAV test_data/MiSeq - - name: HiSeq + - name: Test HiSeq run: multiqc -m SAV test_data/HiSeq - - name: NextSeq + - name: Test NextSeq500 run: multiqc -m SAV test_data/NextSeq500 - - name: NovaSeq + - name: Test NextSeq2000 + run: multiqc -m SAV test_data/NextSeq2000 + + - name: Test NovaSeq run: multiqc -m SAV test_data/NovaSeq diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..05b5cae --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,51 @@ +minimum_pre_commit_version: "2.9.2" + +repos: + # Meta hooks for verification + - repo: meta + hooks: + - id: identity + - id: check-hooks-apply + + # Standard pre-commit hooks + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: "v5.0.0" + hooks: + - id: check-added-large-files + args: ["--maxkb=1000"] + - id: check-merge-conflict + - id: check-yaml + - id: check-toml + - id: debug-statements + - id: end-of-file-fixer + - id: trailing-whitespace + - id: mixed-line-ending + args: ["--fix=lf"] + + # Line ending normalization + - repo: https://github.com/Lucas-C/pre-commit-hooks + rev: "v1.5.5" + hooks: + - id: remove-crlf + + # Prettier for markdown, yaml, html, json formatting + - repo: https://github.com/pre-commit/mirrors-prettier + rev: "v3.1.0" + hooks: + - id: prettier + types_or: [markdown, yaml, html, json] + additional_dependencies: + - "prettier@3.1.0" + + # Ruff formatting + - repo: https://github.com/astral-sh/ruff-pre-commit + rev: "v0.8.3" + hooks: + - id: ruff-format + + # Ruff linting with auto-fix + - repo: https://github.com/astral-sh/ruff-pre-commit + rev: "v0.8.3" + hooks: + - id: ruff + args: [--fix, --exit-non-zero-on-fix] diff --git a/.prettierignore b/.prettierignore new file mode 100644 index 0000000..8cfe595 --- /dev/null +++ b/.prettierignore @@ -0,0 +1,30 @@ +# Build artifacts +dist/ +build/ +*.egg-info/ + +# Python cache +__pycache__/ +*.pyc + +# Test data +test_data/ + +# Virtual environments +venv/ +.venv/ +env/ + +# Coverage +htmlcov/ +.coverage + +# IDE +.idea/ +.vscode/ + +# Example reports +docs/example/ + +# Lock files +*.lock diff --git a/.prettierrc.js b/.prettierrc.js new file mode 100644 index 0000000..ff9d568 --- /dev/null +++ b/.prettierrc.js @@ -0,0 +1,10 @@ +module.exports = { + printWidth: 120, + tabWidth: 2, + useTabs: false, + semi: true, + singleQuote: false, + trailingComma: "all", + bracketSpacing: true, + proseWrap: "preserve", +}; diff --git a/CLAUDE.md b/CLAUDE.md new file mode 100644 index 0000000..bd233bf --- /dev/null +++ b/CLAUDE.md @@ -0,0 +1,131 @@ +# CLAUDE.md + +This file provides guidance for Claude Code (claude.ai/code) when working with the MultiQC_SAV plugin. + +## Project Overview + +MultiQC_SAV is a plugin for [MultiQC](https://multiqc.info/) that parses InterOp files from Illumina sequencers and generates tables and graphs for quality control metrics. It leverages the [Illumina InterOp Python API](https://github.com/Illumina/interop) to read binary metric files. + +## Project Structure + +``` +MultiQC_SAV/ +├── multiqc_sav/ # Main plugin package +│ ├── __init__.py # Package identifier +│ ├── multiqc_sav.py # Plugin hook/config registration +│ └── modules/ +│ └── sav.py # Main SAV module implementation +├── test_data/ # Test datasets for various sequencers +│ ├── HiSeq/ +│ ├── MiSeq/ +│ ├── NextSeq500/ +│ ├── NextSeq2000/ +│ └── NovaSeq/ +├── docs/ # Documentation and example reports +├── .github/workflows/ # CI/CD workflows +│ ├── linux.yaml # Build and test workflow +│ └── lint.yaml # Linting workflow +├── pyproject.toml # Project configuration and dependencies +├── .pre-commit-config.yaml # Pre-commit hooks configuration +├── .prettierrc.js # Prettier formatter config +└── .prettierignore # Prettier exclusions +``` + +## Development Setup + +```bash +# Install in development mode with dev dependencies +pip install -e ".[dev]" + +# Install pre-commit hooks +pre-commit install +``` + +## Common Commands + +```bash +# Run linting +ruff check . +ruff format --check . + +# Auto-fix linting issues +ruff check --fix . +ruff format . + +# Run prettier on markdown/yaml +prettier --check "**/*.{md,yaml,yml,json}" + +# Run tests with test data +multiqc -m SAV test_data/MiSeq +multiqc -m SAV test_data/HiSeq +multiqc -m SAV test_data/NextSeq500 +multiqc -m SAV test_data/NextSeq2000 +multiqc -m SAV test_data/NovaSeq + +# Run all pre-commit hooks +pre-commit run --all-files +``` + +## Code Style Guidelines + +- **Line length**: 120 characters +- **Python version**: 3.9+ +- **Formatting**: Ruff (format + lint) +- **Type hints**: Required for all function signatures +- **Docstrings**: Required for all public functions +- **Imports**: Sorted by isort (via ruff) + +## MultiQC Module Architecture + +### Plugin Registration + +The plugin uses entry points in `pyproject.toml`: + +```toml +[project.entry-points."multiqc.hooks.v1"] +config_loaded = "multiqc_sav.multiqc_sav:update_config" + +[project.entry-points."multiqc.modules.v1"] +SAV = "multiqc_sav.modules.sav:SAV" +``` + +### Hook System + +`multiqc_sav.py` contains the `update_config()` hook which: +- Registers the SAV module in the module order +- Sets module tags (DNA, RNA, BCL, Demultiplex) +- Disables the built-in InterOp module to avoid duplicate data +- Configures search patterns for RunInfo.xml and RunParameters.xml + +### Main Module + +`modules/sav.py` contains the `SAV` class which extends `BaseMultiqcModule`: + +1. **File Discovery**: Uses `find_log_files("SAV/xml")` to locate XML files +2. **Run Info Parsing**: Extracts metadata from RunInfo.xml +3. **Metrics Loading**: Uses InterOp API to read binary metric files +4. **Data Processing**: Parses metrics into pandas DataFrames +5. **Visualization**: Generates MultiQC plots (tables, bargraphs, heatmaps, linegraphs, scatter plots) + +## Supported Sequencers + +- MiSeq +- HiSeq 3000/4000 +- NextSeq 500/2000 +- NovaSeq 6000 + +## Key Dependencies + +- `interop>=1.1.23` - Illumina InterOp Python API for reading binary metrics +- `multiqc>=1.10` - MultiQC framework +- `pandas` - Data manipulation +- `numpy` - Numerical operations + +## Testing + +Tests are run via GitHub Actions on Python 3.9-3.12. Each test verifies that the module can process test data without errors by running MultiQC with the SAV module flag. + +## CI/CD + +- **Build workflow** (`linux.yaml`): Tests installation and module execution +- **Lint workflow** (`lint.yaml`): Runs ruff format check, ruff lint check, and prettier diff --git a/multiqc_sav/modules/sav.py b/multiqc_sav/modules/sav.py index a08d378..81ee2f4 100644 --- a/multiqc_sav/modules/sav.py +++ b/multiqc_sav/modules/sav.py @@ -1,16 +1,18 @@ -#!/usr/bin/env python +"""MultiQC SAV module for parsing Illumina InterOp data.""" +from __future__ import annotations + +import contextlib import glob import logging import os import re import xml.etree.ElementTree as ET -from collections import OrderedDict from datetime import datetime -from typing import Dict +from typing import Any import interop -import numpy +import numpy as np import pandas as pd from interop import py_interop_plot from multiqc import config @@ -18,17 +20,16 @@ from multiqc.plots import bargraph, heatmap, linegraph, scatter, table from multiqc.utils import mqc_colour -# Initialise the main MultiQC logger log = logging.getLogger("multiqc") -HEADERS = { +HEADERS: dict[str, dict[str, Any]] = { "Error Rate": { "title": "Error Rate (%)", "description": "The calculated error rate, as determined by a PhiX spike-in", "min": 0, "max": 100, "suffix": "%", - "format": "{:,.0f}", # No decimal places please + "format": "{:,.0f}", }, "Error Rate 35": { "title": "Error Rate 35 Cycles (%)", @@ -36,7 +37,7 @@ "min": 0, "max": 100, "suffix": "%", - "format": "{:,.0f}", # No decimal places please + "format": "{:,.0f}", "hidden": True, }, "Error Rate 50": { @@ -45,7 +46,7 @@ "min": 0, "max": 100, "suffix": "%", - "format": "{:,.0f}", # No decimal places please + "format": "{:,.0f}", "hidden": True, }, "Error Rate 75": { @@ -54,7 +55,7 @@ "min": 0, "max": 100, "suffix": "%", - "format": "{:,.0f}", # No decimal places please + "format": "{:,.0f}", "hidden": True, }, "Error Rate 100": { @@ -63,7 +64,7 @@ "min": 0, "max": 100, "suffix": "%", - "format": "{:,.0f}", # No decimal places please + "format": "{:,.0f}", "hidden": True, }, "First Cycle Intensity": { @@ -76,7 +77,7 @@ "suffix": "%", "min": 0, "max": 100, - "format": "{:,.0f}", # No decimal places please + "format": "{:,.0f}", }, "% >= Q30": { "title": "% >= Q30", @@ -84,46 +85,41 @@ "min": 0, "max": 100, "suffix": "%", - "format": "{:,.0f}", # No decimal places please + "format": "{:,.0f}", }, "% Occupancy Proxy": { "title": "Occupancy Proxy (%)", - # "description": "", "suffix": "%", - "format": "{:,.0f}", # No decimal places please + "format": "{:,.0f}", }, "% Occupied": { "title": "Occupied (%)", "description": "The percentage of nanowells occupied by clusters, +/- 1 standard deviation.", "suffix": "%", - "format": "{:,.0f}", # No decimal places please + "format": "{:,.0f}", }, "Projected Yield G": { - "title": "Projected Yield ({})".format(config.base_count_prefix), - "description": "The expected number of bases sequenced ({} base pairs over all 'usable cycles'".format( - config.base_count_desc - ), + "title": f"Projected Yield ({config.base_count_prefix})", + "description": f"The expected number of bases sequenced ({config.base_count_desc} base pairs over all 'usable cycles'", "shared_key": "base_count", - "modify": lambda x: (x * 1000000000.0) * config.base_count_multiplier, # number is already in gigabases + "modify": lambda x: (x * 1000000000.0) * config.base_count_multiplier, "hidden": True, }, "Yield G": { - "title": "Yield ({})".format(config.read_count_prefix), - "description": "The number of bases sequenced ({} base pairs over all 'usable cycles'".format( - config.base_count_desc - ), + "title": f"Yield ({config.read_count_prefix})", + "description": f"The number of bases sequenced ({config.base_count_desc} base pairs over all 'usable cycles'", "shared_key": "base_count", - "modify": lambda x: (x * 1000000000.0) * config.base_count_multiplier, # number is already in gigabases + "modify": lambda x: (x * 1000000000.0) * config.base_count_multiplier, }, "Cluster Count": { - "title": "Clusters ({})".format(config.read_count_prefix), - "description": "Number of clusters for each tile ({})".format(config.read_count_desc), + "title": f"Clusters ({config.read_count_prefix})", + "description": f"Number of clusters for each tile ({config.read_count_desc})", "shared_key": "cluster_count", "modify": lambda x: x * config.read_count_multiplier, }, "Cluster Count Pf": { - "title": "Clusters PF ({})".format(config.read_count_prefix), - "description": "Number of clusters PF for each tile ({})".format(config.read_count_desc), + "title": f"Clusters PF ({config.read_count_prefix})", + "description": f"Number of clusters PF for each tile ({config.read_count_desc})", "shared_key": "cluster_count", "modify": lambda x: x * config.read_count_multiplier, }, @@ -133,7 +129,7 @@ "min": 0, "max": 100, "suffix": "%", - "format": "{:,.0f}", # No decimal places please + "format": "{:,.0f}", }, "Density": { "title": "Density", @@ -174,28 +170,32 @@ "hidden": True, }, "Reads": { - "title": "{} Reads".format(config.read_count_prefix), - "description": "The number of reads ({})".format(config.read_count_desc), + "title": f"{config.read_count_prefix} Reads", + "description": f"The number of reads ({config.read_count_desc})", "shared_key": "read_count", "modify": lambda x: x * config.read_count_multiplier, }, "Reads Pf": { - "title": "{} PF Reads".format(config.read_count_prefix), - "description": "The number of passing filter reads ({})".format(config.read_count_desc), + "title": f"{config.read_count_prefix} PF Reads", + "description": f"The number of passing filter reads ({config.read_count_desc})", "shared_key": "read_count", "modify": lambda x: x * config.read_count_multiplier, }, - "Tile Count": {"title": "Tiles", "description": "The number of tiles per lane.", "hidden": True,}, + "Tile Count": { + "title": "Tiles", + "description": "The number of tiles per lane.", + "hidden": True, + }, "Total Pf Reads": { - "title": "{} PF Reads".format(config.read_count_prefix), - "description": "The total number of passing filter reads for this lane ({})".format(config.read_count_desc), + "title": f"{config.read_count_prefix} PF Reads", + "description": f"The total number of passing filter reads for this lane ({config.read_count_desc})", "modify": lambda x: float(x) * config.read_count_multiplier, "format": "{:,.2f}", "shared_key": "read_count", }, "Total Reads": { - "title": "{} Reads".format(config.read_count_prefix), - "description": "The total number of reads for this lane ({})".format(config.read_count_desc), + "title": f"{config.read_count_prefix} Reads", + "description": f"The total number of reads for this lane ({config.read_count_desc})", "modify": lambda x: float(x) * config.read_count_multiplier, "format": "{:,.2f}", "shared_key": "read_count", @@ -203,34 +203,46 @@ "Mapped Reads Cv": { "title": "CV", "description": "The coefficient of variation for the number of counts across all indexes.", - "format": "{:,.2f}", # 2 decimal places please + "format": "{:,.2f}", }, "Max Mapped Reads": { - "title": "{} Max Mapped Reads".format(config.read_count_prefix), - "description": "The highest representation for any index ({})".format(config.read_count_desc), + "title": f"{config.read_count_prefix} Max Mapped Reads", + "description": f"The highest representation for any index ({config.read_count_desc})", "modify": lambda x: float(x) * config.read_count_multiplier, "format": "{:,.2f}", "shared_key": "read_count", }, "Min Mapped Reads": { - "title": "{} Min Mapped Reads".format(config.read_count_prefix), - "description": "The lowest representation for any index ({})".format(config.read_count_desc), + "title": f"{config.read_count_prefix} Min Mapped Reads", + "description": f"The lowest representation for any index ({config.read_count_desc})", "modify": lambda x: float(x) * config.read_count_multiplier, "format": "{:,.2f}", "shared_key": "read_count", }, "Total Fraction Mapped Reads": {"hidden": True}, "Fraction Mapped": {"hidden": True}, - "Index1": {"title": "Index 1 (I7)", "description": "The sequence for the first Index Read.",}, - "Index2": {"title": "Index 2 (I5)", "description": "The sequence for the second Index Read",}, - "Project Name": {"title": "Project Name", "description": "Sample Project Name",}, - "Sample Id": {"title": "Sample ID", "description": "The Sample ID given in the SampleSheet",}, + "Index1": { + "title": "Index 1 (I7)", + "description": "The sequence for the first Index Read.", + }, + "Index2": { + "title": "Index 2 (I5)", + "description": "The sequence for the second Index Read", + }, + "Project Name": { + "title": "Project Name", + "description": "Sample Project Name", + }, + "Sample Id": { + "title": "Sample ID", + "description": "The Sample ID given in the SampleSheet", + }, } class SAV(BaseMultiqcModule): """ - Generate SAV tables an Graphs including: + Generate SAV tables and graphs including: - GRAPH: Intensity/Cycle/Channel - GRAPH: Clusters/Lane - GRAPH: Qscore Heatmap @@ -239,10 +251,11 @@ class SAV(BaseMultiqcModule): - TABLE: Run Summary """ - def __init__(self): - - super(SAV, self).__init__( - name="Illumina SAV", anchor="sav", info=" - Sequencing Metrics from Illumina sequencers", + def __init__(self) -> None: + super().__init__( + name="Illumina SAV", + anchor="sav", + info=" - Sequencing Metrics from Illumina sequencers", ) # Set variables @@ -264,47 +277,41 @@ def __init__(self): illumina_dir = os.path.dirname(run_info_xml) else: log.debug("Skipping MultiQC_SAV, required files were not found or not in the right structure.") - return None + return + self.run_metrics: Any = None self.set_run_info(run_info_xml) self.load_metrics(illumina_dir) self.summary_qc() self.q_summary() self.imaging_qc() - def load_metrics(self, illumina_dir) -> None: + def load_metrics(self, illumina_dir: str) -> None: + """Load run metrics from InterOp directory.""" log.info("Loading Run Metrics") - self.run_metrics = interop.read(run=illumina_dir, valid_to_load=interop.load_imaging_metrics(), finalize=True,) + self.run_metrics = interop.read( + run=illumina_dir, + valid_to_load=interop.load_imaging_metrics(), + finalize=True, + ) ############# # RUN INFO ############# def set_run_info(self, run_info_xml: str) -> None: + """Parse and display run information from RunInfo.xml.""" log.info("Loading Run Info") - run_info_xml = ET.parse(run_info_xml) - root = run_info_xml.getroot() + tree = ET.parse(run_info_xml) + root = tree.getroot() for run in root: run_number = run.attrib["Number"] - flowcell = [fc.text for fc in run.iter("Flowcell")][0] - instrument_id = [fc.text for fc in run.iter("Instrument")][0] - run_date = [fc.text for fc in run.iter("Date")][0] - try: - # MiSeq/NextSeq500/HiSeq3000 - parsed_run_date = datetime.strftime(datetime.strptime(run_date, "%y%m%d"), "%d-%m-%Y") - except ValueError: - try: - # NovaSeq6000 - parsed_run_date = datetime.strftime(datetime.strptime(run_date, "%m/%d/%Y %I:%M:%S %p"), "%d-%m-%Y") - except ValueError: - try: - # NextSeq2000 - parsed_run_date = datetime.strftime( - datetime.strptime(run_date, "%Y-%m-%dT%H:%M:%SZ"), "%d-%m-%Y" - ) - except ValueError: - parsed_run_date = run_date + flowcell = next(fc.text for fc in run.iter("Flowcell")) + instrument_id = next(fc.text for fc in run.iter("Instrument")) + run_date = next(fc.text for fc in run.iter("Date")) + + parsed_run_date = self._parse_run_date(run_date) read_info = "" for read in run.iter("Read"): @@ -341,16 +348,36 @@ def set_run_info(self, run_info_xml: str) -> None: """, ) + def _parse_run_date(self, run_date: str) -> str: + """ + Parse run date from various Illumina sequencer formats. + + Supported formats: + - MiSeq/NextSeq500/HiSeq3000: YYMMDD + - NovaSeq6000: M/D/YYYY H:MM:SS AM/PM + - NextSeq2000: YYYY-MM-DDTHH:MM:SSZ + """ + date_formats = [ + ("%y%m%d", "%d-%m-%Y"), # MiSeq/NextSeq500/HiSeq3000 + ("%m/%d/%Y %I:%M:%S %p", "%d-%m-%Y"), # NovaSeq6000 + ("%Y-%m-%dT%H:%M:%SZ", "%d-%m-%Y"), # NextSeq2000 + ] + + for input_fmt, output_fmt in date_formats: + try: + return datetime.strftime(datetime.strptime(run_date, input_fmt), output_fmt) + except ValueError: + continue + + # Return raw date if no format matched + return run_date + ############# # SUMMARY QC ############# def summary_qc(self) -> None: - """ - Generate MultiQC sections related to Summary tables - - :return: None - """ + """Generate MultiQC sections related to Summary tables.""" log.info("Gathering Read summary metrics") summary_read = pd.DataFrame(interop.summary(self.run_metrics, level="Read")) summary_nonindex = pd.DataFrame(interop.summary(self.run_metrics, level="NonIndex")) @@ -383,29 +410,24 @@ def summary_qc(self) -> None: ) def parse_read_summary( - self, read_metrics: pd.DataFrame, non_index_metrics: pd.DataFrame, total_metrics: pd.DataFrame - ) -> Dict: - """ - Parse "Read Summary" table DataFrame - - :return: Dict containing table data - """ - table_data: dict = self._parse_reads(read_metrics) - - for read, data in non_index_metrics.iterrows(): + self, + read_metrics: pd.DataFrame, + non_index_metrics: pd.DataFrame, + total_metrics: pd.DataFrame, + ) -> dict[str, dict[str, Any]]: + """Parse "Read Summary" table DataFrame.""" + table_data: dict[str, dict[str, Any]] = self._parse_reads(read_metrics) + + for _read, data in non_index_metrics.iterrows(): table_data["Non-Indexed"] = data.to_dict() - for read, data in total_metrics.iterrows(): + for _read, data in total_metrics.iterrows(): table_data["Total"] = data.to_dict() return table_data - def read_summary_table(self, data: pd.DataFrame) -> table.plot: - """ - Format "Read Summary" data dict and add plot config. - - :return: table object to be used in a MultiQC section - """ + def read_summary_table(self, data: dict[str, dict[str, Any]]) -> table.plot: + """Format "Read Summary" data dict and add plot config.""" headers = {header: HEADERS[header] for header in interop.summary_columns(level="Lane")} table_config = { @@ -416,28 +438,18 @@ def read_summary_table(self, data: pd.DataFrame) -> table.plot: return table.plot(data, headers, table_config) - def parse_lane_summary(self, data: pd.DataFrame) -> Dict: - """ - Parse "Lane Summary" table DataFrame - - :return: Dict containing table data - """ + def parse_lane_summary(self, data: pd.DataFrame) -> dict[str, dict[str, Any]]: + """Parse "Lane Summary" table DataFrame.""" lanes = data.groupby("Lane") - table_data: dict = {} + table_data: dict[str, dict[str, Any]] = {} for lane, reads in lanes: - lane_data = {} reads_dict = self._parse_reads(reads, key_prefix=f"Lane {lane}") table_data.update(reads_dict) return table_data - def lane_summary_table(self, data: Dict) -> table.plot: - """ - Format "Lane Summary" data dict and add plot config. - - :return: table object to be used in a MultiQC section - """ - + def lane_summary_table(self, data: dict[str, dict[str, Any]]) -> table.plot: + """Format "Lane Summary" data dict and add plot config.""" headers = {header: HEADERS[header] for header in interop.summary_columns(level="Lane")} table_config = { "namespace": "SAV", @@ -445,43 +457,40 @@ def lane_summary_table(self, data: Dict) -> table.plot: "col1_header": "Lane - Read", } - return table.plot(data, headers, table_config,) - - def clusters_lane_plot(self, data: Dict) -> bargraph.plot: - """ - Format "Clusters per Lane" data dict and add plot config. + return table.plot(data, headers, table_config) - :return: bar plot object to be used in a MultiQC section - """ + def clusters_lane_plot(self, data: dict[str, dict[str, Any]]) -> bargraph.plot: + """Format "Clusters per Lane" data dict and add plot config.""" + cluster_data: dict[str, dict[str, float]] = {} + read_data: dict[str, dict[str, float]] = {} - cluster_data = {} - read_data = {} - for key, value in data.items(): + for value in data.values(): lane = int(value["Lane"]) - if f"Lane {lane}" not in cluster_data: - cluster_data[f"Lane {lane}"] = { + lane_key = f"Lane {lane}" + + if lane_key not in cluster_data: + cluster_data[lane_key] = { "clusters": value["Cluster Count"], "clusters_pf": value["Cluster Count Pf"], "clusters_diff": value["Cluster Count"] - value["Cluster Count Pf"], } - read_data[f"Lane {lane}"] = { + read_data[lane_key] = { "reads": value["Reads"], "reads_pf": value["Reads Pf"], "reads_diff": value["Reads"] - value["Reads Pf"], } else: - cluster_data[f"Lane {lane}"]["clusters"] += value["Cluster Count"] - cluster_data[f"Lane {lane}"]["clusters_pf"] += value["Cluster Count Pf"] - cluster_data[f"Lane {lane}"]["clusters_diff"] += value["Cluster Count"] - value["Cluster Count Pf"] - read_data[f"Lane {lane}"]["reads"] += value["Reads"] - read_data[f"Lane {lane}"]["reads_pf"] += value["Reads Pf"] - read_data[f"Lane {lane}"]["reads_diff"] += value["Reads"] - value["Reads Pf"] - - cats = [OrderedDict(), OrderedDict()] - cats[0]["clusters_pf"] = {"name": "Clusters PF"} - cats[0]["clusters_diff"] = {"name": "Clusters not PF"} - cats[1]["reads_pf"] = {"name": "Reads PF"} - cats[1]["reads_diff"] = {"name": "Reads not PF"} + cluster_data[lane_key]["clusters"] += value["Cluster Count"] + cluster_data[lane_key]["clusters_pf"] += value["Cluster Count Pf"] + cluster_data[lane_key]["clusters_diff"] += value["Cluster Count"] - value["Cluster Count Pf"] + read_data[lane_key]["reads"] += value["Reads"] + read_data[lane_key]["reads_pf"] += value["Reads Pf"] + read_data[lane_key]["reads_diff"] += value["Reads"] - value["Reads Pf"] + + cats = [ + {"clusters_pf": {"name": "Clusters PF"}, "clusters_diff": {"name": "Clusters not PF"}}, + {"reads_pf": {"name": "Reads PF"}, "reads_diff": {"name": "Reads not PF"}}, + ] plot_config = { "id": "sav-summary-clusters-reads-lane-plot", @@ -492,30 +501,29 @@ def clusters_lane_plot(self, data: Dict) -> bargraph.plot: return bargraph.plot([cluster_data, read_data], cats, plot_config) - def _parse_reads(self, reads_df: pd.DataFrame, key_prefix: str = None) -> Dict: - """ - Utility function to parse a "Reads" dataframe to dict - - :return: Reads dict - """ - reads_dict = {} + def _parse_reads( + self, + reads_df: pd.DataFrame, + key_prefix: str | None = None, + ) -> dict[str, dict[str, Any]]: + """Parse a "Reads" dataframe to dict.""" + reads_dict: dict[str, dict[str, Any]] = {} reads_df = reads_df.set_index("ReadNumber") + for read, data in reads_df.iterrows(): key = f"Read {read}" + " (I)" if data["IsIndex"] == 89 else f"Read {read}" if key_prefix: key = f"{key_prefix} - {key}" reads_dict[key] = data.drop("IsIndex").to_dict() + return reads_dict ############# # Q SUMMARY ############# - def q_summary(self) -> None: - """ - Generate MultiQC sections related to Qscore - :return: None - """ + def q_summary(self) -> None: + """Generate MultiQC sections related to Qscore.""" # - GRAPH: Qscore Heatmap log.info("Generating 'Qscore Heatmap' plot") self.add_section( @@ -530,28 +538,31 @@ def q_summary(self) -> None: self.add_section( name="Qscore Histogram", anchor="sav-qscore-histogram", - description="Qscore Histogram graphs the number of bases by quality score. The quality score is cumulative for the current cycle. Only bases from reads that pass the quality filter are included.", + description=( + "Qscore Histogram graphs the number of bases by quality score. " + "The quality score is cumulative for the current cycle. " + "Only bases from reads that pass the quality filter are included." + ), plot=self.qscore_histogram_plot(), ) def qscore_heatmap_plot(self) -> heatmap.plot: """ - Get heatmap data from run_metrics object - Note: this function has *much* room for improvement, but we need to wait for further developments in the InterOp library. - In the mean time, this will have to do. + Get heatmap data from run_metrics object. - :return: heatmap plot object to be used in a MultiQC section + Note: this function has room for improvement, but we need to wait + for further developments in the InterOp library. """ options = py_interop_plot.filter_options(self.run_metrics.run_info().flowcell().naming_method()) rows = py_interop_plot.count_rows_for_heatmap(self.run_metrics) cols = py_interop_plot.count_columns_for_heatmap(self.run_metrics) - dataBuffer = numpy.zeros((rows, cols), dtype=numpy.float32) + data_buffer = np.zeros((rows, cols), dtype=np.float32) data = py_interop_plot.heatmap_data() - try: - py_interop_plot.plot_qscore_heatmap(self.run_metrics, options, data, dataBuffer.ravel()) - except py_interop_plot.invalid_filter_option: - pass - plot_data = dataBuffer.transpose().tolist() + + with contextlib.suppress(py_interop_plot.invalid_filter_option): + py_interop_plot.plot_qscore_heatmap(self.run_metrics, options, data, data_buffer.ravel()) + + plot_data = data_buffer.transpose().tolist() # cycles x_cats = list(range(0, cols)) # qscore @@ -581,20 +592,20 @@ def qscore_heatmap_plot(self) -> heatmap.plot: def qscore_histogram_plot(self) -> linegraph.plot: """ - Get histogram data from run_metrics object - Note: this function has *much* room for improvement, but we need to wait for further developments in the InterOp library - In the mean time, this will have to do. + Get histogram data from run_metrics object. - :return: linegraph plot object to be used in a MultiQC section + Note: this function has room for improvement, but we need to wait + for further developments in the InterOp library. """ bar_data = py_interop_plot.bar_plot_data() options = py_interop_plot.filter_options(self.run_metrics.run_info().flowcell().naming_method()) py_interop_plot.plot_qscore_histogram(self.run_metrics, options, bar_data) - hist = {} - qscore = [] - reads = [] - binsize = [] + hist: dict[float, float] = {} + qscore: list[float] = [] + reads: list[float] = [] + binsize: list[float] = [] + for i in range(bar_data.size()): qscore = [bar_data.at(i).at(j).x() for j in range(bar_data.at(i).size())] reads = [bar_data.at(i).at(j).y() for j in range(bar_data.at(i).size())] @@ -604,9 +615,10 @@ def qscore_histogram_plot(self) -> linegraph.plot: while i < len(qscore): j = 0 while j < binsize[i]: - hist.update({qscore[i] + j: reads[i]}) + hist[qscore[i] + j] = reads[i] j += 1 i += 1 + plot_data = {bar_data.title(): hist} plot_config = { @@ -620,14 +632,14 @@ def qscore_histogram_plot(self) -> linegraph.plot: ############# # IMAGING QC ############# + def imaging_qc(self) -> None: """ Generate MultiQC sections related to Imaging. + This includes: - Plot: Intensity/Cycle/Channel - Plot: %Occ/%PF - - :return: None """ log.info("Gathering Imaging metrics") imaging = pd.DataFrame(interop.imaging(self.run_metrics)) @@ -641,7 +653,7 @@ def imaging_qc(self) -> None: name="Intensity per Cycle", anchor="sav-intensity-cycle", description="Intensity by color and cycle of the 90% percentile of the data for each tile", - plot=self.intensity_cycle_plot(plot_data.get("intensity_cycle", [])), + plot=self.intensity_cycle_plot(plot_data.get("intensity_cycle", {})), ) # - GRAPH: %Occ/%PF @@ -651,48 +663,55 @@ def imaging_qc(self) -> None: name="% PF vs % Occupied", anchor="sav-imaging-pf-vs-occ", description="% Clusters passing filter vs % Wells Occupied", - plot=self.occ_vs_pf_plot(plot_data.get("occ_vs_pf", [])), + plot=self.occ_vs_pf_plot(plot_data.get("occ_vs_pf", {})), ) - def parse_imaging_table(self, data: pd.DataFrame) -> Dict: + def parse_imaging_table(self, data: pd.DataFrame) -> dict[str, Any]: """ - Parse full imaging table DataFrame + Parse full imaging table DataFrame. - :return: Dict containing data for intesity per cylce plot (key:"intensity_cycle") and %occ vs %pf plot (key: ""occ_vs_pf") + Returns dict containing data for intensity per cycle plot (key: "intensity_cycle") + and %occ vs %pf plot (key: "occ_vs_pf"). """ # set color scale for occ_pf cscale = mqc_colour.mqc_colour_scale() colors = cscale.get_colours("Dark2") per_lane = data.groupby("Lane") - occ_pf = {} - intensity_cycle = {} - for lane, lane_data in per_lane: - lane = int(lane) + occ_pf: dict[str, list[dict[str, Any]]] = {} + intensity_cycle: dict[str, dict[int, float]] = {} + + for lane_num, lane_data in per_lane: + lane = int(lane_num) # prep intensity_cycle - CHANNEL_SETS = [{"P90/RED", "P90/GREEN"}, {"P90/Red", "P90/Green"}, {"P90/G", "P90/A", "P90/T", "P90/C"}] - channels = set() - for channel_set in CHANNEL_SETS: + channel_sets = [ + {"P90/RED", "P90/GREEN"}, + {"P90/Red", "P90/Green"}, + {"P90/G", "P90/A", "P90/T", "P90/C"}, + ] + channels: set[str] = set() + for channel_set in channel_sets: if channel_set.issubset(lane_data.columns): channels = channel_set # prep occ_pf - if not f"Lane {lane}" in occ_pf: - occ_pf[f"Lane {lane}"] = [] - prev_occ = 0 - prev_pf = 0 + lane_key = f"Lane {lane}" + if lane_key not in occ_pf: + occ_pf[lane_key] = [] + prev_occ = 0.0 + prev_pf = 0.0 # parse imaging table lane for _, row in lane_data.iterrows(): - # intensity_cyle + # intensity_cycle cycle = int(row["Cycle"]) for channel in channels: intensity = float(row[channel]) - if not channel in intensity_cycle: + if channel not in intensity_cycle: intensity_cycle[channel] = {} - if not cycle in intensity_cycle[channel]: - intensity_cycle[channel].update({cycle: 0}) + if cycle not in intensity_cycle[channel]: + intensity_cycle[channel][cycle] = 0 intensity_cycle[channel][cycle] += intensity # occ_pf @@ -703,21 +722,16 @@ def parse_imaging_table(self, data: pd.DataFrame) -> Dict: if occ != prev_occ or pf != prev_pf: prev_occ = occ prev_pf = pf - occ_pf[f"Lane {lane}"].append({"x": occ, "y": pf, "color": colors[lane]}) + occ_pf[lane_key].append({"x": occ, "y": pf, "color": colors[lane]}) else: occ_pf = {} return {"intensity_cycle": intensity_cycle, "occ_vs_pf": occ_pf} - def intensity_cycle_plot(self, data: Dict) -> linegraph.plot: - """ - Format Intensity per Cycle data dict and add plot config. - - :return: linegraph plot object to be used in a MultiQC section - """ - + def intensity_cycle_plot(self, data: dict[str, dict[int, float]]) -> linegraph.plot: + """Format Intensity per Cycle data dict and add plot config.""" # get keys from data - key_color_dict = {} + key_color_dict: dict[str, str] = {} for key in data: if re.match(r"\w+/red", key, re.IGNORECASE): key_color_dict[key] = "red" @@ -742,13 +756,8 @@ def intensity_cycle_plot(self, data: Dict) -> linegraph.plot: return linegraph.plot(data, plot_config) - def occ_vs_pf_plot(self, data: Dict) -> scatter.plot: - """ - Format %Occ vs %PF data dict and add plot config. - - :return: scatter plot object to be used in a MultiQC section - """ - + def occ_vs_pf_plot(self, data: dict[str, list[dict[str, Any]]]) -> scatter.plot: + """Format %Occ vs %PF data dict and add plot config.""" plot_config = { "id": "sav-pf-vs-occ-plot", "title": "SAV: % Passing Filter vs % Occupied", diff --git a/multiqc_sav/multiqc_sav.py b/multiqc_sav/multiqc_sav.py index ddba78f..211833c 100644 --- a/multiqc_sav/multiqc_sav.py +++ b/multiqc_sav/multiqc_sav.py @@ -1,27 +1,27 @@ -#!/usr/bin/env python +"""MultiQC SAV plugin configuration and hooks.""" import logging +from importlib.metadata import version from multiqc.utils import config -from pkg_resources import get_distribution -# Initialise the main MultiQC logger log = logging.getLogger("multiqc") -# Save this plugin's version number (defined in setup.py) to the MultiQC config -config.multiqc_sav_version = get_distribution("multiqc_sav").version -log.info("Running MultiQC SAV Plugin v{}".format(config.multiqc_sav_version)) +# Save this plugin's version number to the MultiQC config +config.multiqc_sav_version = version("multiqc_sav") +log.info(f"Running MultiQC SAV Plugin v{config.multiqc_sav_version}") def update_config() -> None: """ - Update MultiQC config object - * Update module order - * Disable unnecessary modules to avoid duplicate data - * Update search patterns - """ + Update MultiQC config object. + - Update module order + - Disable unnecessary modules to avoid duplicate data + - Update search patterns + """ log.debug("SAV - Updating config") + # Add module to module order config.module_order.append({"SAV": {"module_tag": ["DNA", "RNA", "BCL", "Demultiplex"]}}) @@ -35,5 +35,7 @@ def update_config() -> None: # Update search patterns if "SAV/xml" not in config.sp: - config.update_dict(config.sp, {"SAV/xml": {"fn_re": ".*([Rr]un[Ii]nfo|[Rr]un[Pp]arameters)\.xml", "shared": True}}) + config.update_dict( + config.sp, {"SAV/xml": {"fn_re": ".*([Rr]un[Ii]nfo|[Rr]un[Pp]arameters)\\.xml", "shared": True}} + ) config.update_dict(config.sp, {"bclconvert/runinfo": {"fn": "RunInfo.xml", "shared": True}}) diff --git a/pyproject.toml b/pyproject.toml index 90a6b56..d0f10fb 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,4 +1,100 @@ -[tool.black] +[build-system] +requires = ["setuptools>=61.0"] +build-backend = "setuptools.build_meta" + +[project] +name = "multiqc_sav" +version = "0.0.4" +description = "MultiQC plugin for Illumina SAV Graphs and tables" +readme = "README.md" +license = { text = "MIT" } +authors = [{ name = "Matthias De Smet", email = "11850640+matthdsm@users.noreply.github.com" }] +keywords = ["bioinformatics", "illumina", "sequencing", "quality-control", "multiqc"] +requires-python = ">=3.9" +classifiers = [ + "Development Status :: 4 - Beta", + "Environment :: Console", + "Environment :: Web Environment", + "Intended Audience :: Science/Research", + "License :: OSI Approved :: MIT License", + "Natural Language :: English", + "Operating System :: MacOS :: MacOS X", + "Operating System :: POSIX", + "Operating System :: Unix", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Topic :: Scientific/Engineering", + "Topic :: Scientific/Engineering :: Bio-Informatics", + "Topic :: Scientific/Engineering :: Visualization", +] +dependencies = [ + "interop>=1.1.23", + "multiqc>=1.10", + "pandas", + "numpy", +] + +[project.optional-dependencies] +dev = [ + "pre-commit", + "ruff", + "mypy", + "pytest", + "pandas-stubs", +] + +[project.urls] +Homepage = "https://github.com/MultiQC/MultiQC_SAV" +Repository = "https://github.com/MultiQC/MultiQC_SAV" +Issues = "https://github.com/MultiQC/MultiQC_SAV/issues" + +[project.entry-points."multiqc.hooks.v1"] +config_loaded = "multiqc_sav.multiqc_sav:update_config" + +[project.entry-points."multiqc.modules.v1"] +SAV = "multiqc_sav.modules.sav:SAV" + +[tool.setuptools.packages.find] +include = ["multiqc_sav*"] + +[tool.ruff] line-length = 120 -target_version = ['py36','py37','py38'] +target-version = "py39" + +[tool.ruff.lint] +select = [ + "E", # pycodestyle errors + "W", # pycodestyle warnings + "F", # pyflakes + "I", # isort + "B", # flake8-bugbear + "C4", # flake8-comprehensions + "UP", # pyupgrade + "ARG", # flake8-unused-arguments + "SIM", # flake8-simplify +] +ignore = [ + "E501", # line too long (handled by formatter) + "B008", # do not perform function calls in argument defaults + "B905", # zip without strict parameter + "ARG001", # unused function argument (common in MultiQC modules) + "ARG002", # unused method argument +] + +[tool.ruff.lint.isort] +known-first-party = ["multiqc_sav"] + +[tool.ruff.format] +quote-style = "double" +indent-style = "space" +skip-magic-trailing-comma = false +line-ending = "auto" +[tool.mypy] +python_version = "3.9" +warn_return_any = true +warn_unused_configs = true +ignore_missing_imports = true diff --git a/setup.py b/setup.py index 2f6c65e..de2040c 100755 --- a/setup.py +++ b/setup.py @@ -1,43 +1,5 @@ -#!/usr/bin/env python -""" -MultiQC_SAV is a plugin for MultiQC, leveraging the [InterOp python API](https://github.com/Illumina/interop) -to generate the most used tables and graphs from the Illumina SAV -""" +"""Minimal setup.py for backwards compatibility with older pip versions.""" -from setuptools import setup, find_packages +from setuptools import setup -version = "0.0.3" - -setup( - name="multiqc_sav", - version=version, - author="Matthias De Smet", - author_email="11850640+matthdsm@users.noreply.github.com", - description="MultiQC plugin for Illumina SAV Graphs and tables", - long_description=__doc__, - keywords="bioinformatics", - url="https://github.com/MultiQC/MultiQC_SAV", - license="MIT", - packages=find_packages(), - include_package_data=True, - install_requires=["interop>=1.1.23", "multiqc>=1.10", "pandas"], - entry_points={ - "multiqc.hooks.v1": ["config_loaded = multiqc_sav.multiqc_sav:update_config",], - "multiqc.modules.v1": ["SAV = multiqc_sav.modules.sav:SAV",], - }, - classifiers=[ - "Development Status :: 4 - Beta", - "Environment :: Console", - "Environment :: Web Environment", - "Intended Audience :: Science/Research", - "License :: OSI Approved :: MIT License", - "Natural Language :: English", - "Operating System :: MacOS :: MacOS X", - "Operating System :: POSIX", - "Operating System :: Unix", - "Programming Language :: Python", - "Topic :: Scientific/Engineering", - "Topic :: Scientific/Engineering :: Bio-Informatics", - "Topic :: Scientific/Engineering :: Visualization", - ], -) +setup() From d104fb013f366a97990fe682ee35c6d203f599bb Mon Sep 17 00:00:00 2001 From: Claude Date: Tue, 16 Dec 2025 18:35:05 +0000 Subject: [PATCH 2/9] ci: use pre-commit action for linting workflow Replace separate ruff and prettier jobs with the official pre-commit action. This ensures CI matches local pre-commit results exactly. --- .github/workflows/lint.yaml | 36 ++++-------------------------------- 1 file changed, 4 insertions(+), 32 deletions(-) diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml index 0df3ac6..39f641b 100644 --- a/.github/workflows/lint.yaml +++ b/.github/workflows/lint.yaml @@ -6,8 +6,8 @@ on: pull_request: jobs: - lint: - name: Lint + pre-commit: + name: Pre-commit runs-on: ubuntu-latest timeout-minutes: 5 @@ -20,33 +20,5 @@ jobs: with: python-version: "3.11" - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install ruff - - - name: Ruff format check - run: ruff format --check . - - - name: Ruff lint check - run: ruff check . - - prettier: - name: Prettier - runs-on: ubuntu-latest - timeout-minutes: 5 - - steps: - - name: Checkout code - uses: actions/checkout@v4 - - - name: Set up Node.js - uses: actions/setup-node@v4 - with: - node-version: "20" - - - name: Install Prettier - run: npm install -g prettier@3.1.0 - - - name: Run Prettier check - run: prettier --check "**/*.{md,yaml,yml,json,html}" --ignore-path .prettierignore + - name: Run pre-commit + uses: pre-commit/action@v3.0.1 From 5ff8f9b076bbbfdceb866481f0b6751f4acae6e7 Mon Sep 17 00:00:00 2001 From: Claude Date: Tue, 16 Dec 2025 18:37:31 +0000 Subject: [PATCH 3/9] chore: simplify ruff and mypy configuration Remove redundant options that match defaults: - target-version (inferred from requires-python) - format options (all defaults) - isort section (not needed) - excessive lint rules Keep only essential settings: - line-length = 120 - select core rules (E, F, W, I, UP, SIM) - ignore E501 (handled by formatter) --- pyproject.toml | 33 ++------------------------------- 1 file changed, 2 insertions(+), 31 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index d0f10fb..ded3ae9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -62,39 +62,10 @@ include = ["multiqc_sav*"] [tool.ruff] line-length = 120 -target-version = "py39" [tool.ruff.lint] -select = [ - "E", # pycodestyle errors - "W", # pycodestyle warnings - "F", # pyflakes - "I", # isort - "B", # flake8-bugbear - "C4", # flake8-comprehensions - "UP", # pyupgrade - "ARG", # flake8-unused-arguments - "SIM", # flake8-simplify -] -ignore = [ - "E501", # line too long (handled by formatter) - "B008", # do not perform function calls in argument defaults - "B905", # zip without strict parameter - "ARG001", # unused function argument (common in MultiQC modules) - "ARG002", # unused method argument -] - -[tool.ruff.lint.isort] -known-first-party = ["multiqc_sav"] - -[tool.ruff.format] -quote-style = "double" -indent-style = "space" -skip-magic-trailing-comma = false -line-ending = "auto" +select = ["E", "F", "W", "I", "UP", "SIM"] +ignore = ["E501"] # line length handled by formatter [tool.mypy] -python_version = "3.9" -warn_return_any = true -warn_unused_configs = true ignore_missing_imports = true From 0adedea0e2abb696802c023601a6fc5219c3ba67 Mon Sep 17 00:00:00 2001 From: Claude Date: Tue, 16 Dec 2025 18:41:51 +0000 Subject: [PATCH 4/9] fix: wrap long description strings to satisfy line length limit Remove E501 ignore rule - fix the actual long lines instead of ignoring them. --- multiqc_sav/modules/sav.py | 22 +++++++++++++++++----- pyproject.toml | 1 - 2 files changed, 17 insertions(+), 6 deletions(-) diff --git a/multiqc_sav/modules/sav.py b/multiqc_sav/modules/sav.py index 81ee2f4..c3cdc56 100644 --- a/multiqc_sav/modules/sav.py +++ b/multiqc_sav/modules/sav.py @@ -100,7 +100,9 @@ }, "Projected Yield G": { "title": f"Projected Yield ({config.base_count_prefix})", - "description": f"The expected number of bases sequenced ({config.base_count_desc} base pairs over all 'usable cycles'", + "description": ( + f"The expected number of bases sequenced ({config.base_count_desc} base pairs over all 'usable cycles'" + ), "shared_key": "base_count", "modify": lambda x: (x * 1000000000.0) * config.base_count_multiplier, "hidden": True, @@ -133,17 +135,24 @@ }, "Density": { "title": "Density", - "description": "The density of clusters (in thousands per mm2) detected by image analysis, +/- 1 standard deviation.", + "description": ( + "The density of clusters (in thousands per mm2) detected by image analysis, +/- 1 standard deviation." + ), "hidden": True, }, "Density Pf": { "title": "Density PF", - "description": "The density of clusters PF (in thousands per mm2) detected by image analysis, +/- 1 standard deviation.", + "description": ( + "The density of clusters PF (in thousands per mm2) detected by image analysis, +/- 1 standard deviation." + ), "hidden": True, }, "Phasing": { "title": "Phasing", - "description": "The value used by RTA for the percentage of molecules in a cluster for which sequencing falls behind (phasing) the current cycle within a read.", + "description": ( + "The value used by RTA for the percentage of molecules in a cluster " + "for which sequencing falls behind (phasing) the current cycle within a read." + ), }, "Phasing Offset": { "title": "Phasing Offset", @@ -157,7 +166,10 @@ }, "Prephasing": { "title": "Prephasing", - "description": "The value used by RTA for the percentage of molecules in a cluster for which sequencing jumps ahead (prephasing) the current cycle within a read.", + "description": ( + "The value used by RTA for the percentage of molecules in a cluster " + "for which sequencing jumps ahead (prephasing) the current cycle within a read." + ), }, "Prephasing Offset": { "title": "Prephasing Offset", diff --git a/pyproject.toml b/pyproject.toml index ded3ae9..ac58368 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -65,7 +65,6 @@ line-length = 120 [tool.ruff.lint] select = ["E", "F", "W", "I", "UP", "SIM"] -ignore = ["E501"] # line length handled by formatter [tool.mypy] ignore_missing_imports = true From 2692f892adaf44b409d559fe081bc864a19ef6a3 Mon Sep 17 00:00:00 2001 From: Claude Date: Wed, 17 Dec 2025 09:11:31 +0000 Subject: [PATCH 5/9] style: apply pre-commit fixes - Fix end-of-file newlines in XML files - Fix trailing whitespace in HTML reports - Normalize line endings (CRLF to LF) - Apply prettier formatting to CLAUDE.md --- .gitignore | 2 +- CLAUDE.md | 1 + docs/example/NextSeq500_report.html | 282 +- docs/example/NovaSeq_report.html | 286 +- test_data/HiSeq/RunInfo.xml | 1844 +++---- test_data/HiSeq/RunParameters.xml | 250 +- test_data/MiSeq/CompletedJobInfo.xml | 210 +- .../MiSeq/GenerateFASTQRunStatistics.xml | 4726 ++++++++--------- test_data/MiSeq/RunCompletionStatus.xml | 24 +- test_data/MiSeq/RunInfo.xml | 30 +- test_data/MiSeq/RunParameters.xml | 184 +- test_data/NextSeq2000/RunCompletionStatus.xml | 2 +- test_data/NextSeq2000/RunInfo.xml | 1 - test_data/NextSeq2000/RunParameters.xml | 2 +- test_data/NextSeq500/RTAConfiguration.xml | 282 +- test_data/NextSeq500/RunCompletionStatus.xml | 36 +- test_data/NextSeq500/RunInfo.xml | 1776 +++---- test_data/NextSeq500/RunParameters.xml | 1922 +++---- test_data/NovaSeq/RunParameters.xml | 282 +- 19 files changed, 6071 insertions(+), 6071 deletions(-) diff --git a/.gitignore b/.gitignore index ec6d653..b0e2826 100644 --- a/.gitignore +++ b/.gitignore @@ -139,4 +139,4 @@ data # MacOS cruft .DS_Store -workspace.code* \ No newline at end of file +workspace.code* diff --git a/CLAUDE.md b/CLAUDE.md index bd233bf..186e997 100644 --- a/CLAUDE.md +++ b/CLAUDE.md @@ -92,6 +92,7 @@ SAV = "multiqc_sav.modules.sav:SAV" ### Hook System `multiqc_sav.py` contains the `update_config()` hook which: + - Registers the SAV module in the module order - Sets module tags (DNA, RNA, BCL, Demultiplex) - Disables the built-in InterOp module to avoid duplicate data diff --git a/docs/example/NextSeq500_report.html b/docs/example/NextSeq500_report.html index 5db24cb..1e718c6 100644 --- a/docs/example/NextSeq500_report.html +++ b/docs/example/NextSeq500_report.html @@ -12,7 +12,7 @@ http://multiqc.info --> - + @@ -40,7 +40,7 @@ - + @@ -5040,52 +5040,52 @@

- +

Loading report..

@@ -5121,7 +5121,7 @@

Highlight Samples

- +
@@ -5141,7 +5141,7 @@

Rename Samples

- + @@ -5170,7 +5170,7 @@

Show / Hide Samples

- +
@@ -5183,7 +5183,7 @@

- +

Regex mode off @@ -5255,9 +5255,9 @@

Export Plots

- +

Note that additional data was saved in multiqc_data when this report was generated.

- +
@@ -5337,7 +5337,7 @@

About MultiQC

- +

@@ -5375,15 +5375,15 @@

JavaScript Disabled

Report - + generated on 2021-05-18, 09:20 - - + + based on data in: - + /Users/matdsmet/Projects/MultiQC_SAV/test_data/NextSeq500

- - + +
@@ -5396,33 +5396,33 @@

JavaScript Disabled

- - - + + +

Illumina SAV

Illumina SAV - Sequencing Metrics from Illumina sequencers

- - - - + + + +
- +

Run Info - +

- - - - + + + +
- +
@@ -5442,42 +5442,42 @@

Settings

- +
- - - - + + + +
- +

Summary Read Metrics - +

- +

Summary metrics per Read

- - + +
- + - + - + - + Showing 5/5 rows and 6/7 columns. - +
@@ -5509,7 +5509,7 @@

Sav-Read-Metrics-Summary-Table: Columns

- +
|| @@ -5592,42 +5592,42 @@

Sav-Read-Metrics-Summary-Table: Columns

- +
- - - - + + + +
- +

Summary Lane Metrics - +

- +

Summary metrics per Lane per Read

- - + +
- + - + - + - + Showing 12/12 rows and 13/24 columns. - +
@@ -5659,7 +5659,7 @@

Sav-Lane-Metrics-Summary-Table: Columns

- +
|| @@ -5929,26 +5929,26 @@

Sav-Lane-Metrics-Summary-Table: Columns

- +
- - - - + + + +
- +

Clusters/Reads per Lane - +

- +

Total Cluster/Read count per Lane

- - -
- - + + +
+ +
   
@@ -5957,101 +5957,101 @@

loading..

- +
- - - - + + + +
- +

Qscore Heatmap - +

- +

The Qscore Heat Map provides an overview of quality scores across cycles.

- - + +
-
loading..
+
loading..
- +
- - - - + + + +
- +

Qscore Histogram - +

- +

Qscore Histogram graphs the number of bases by quality score. The quality score is cumulative for the current cycle. Only bases from reads that pass the quality filter are included.

- - -
loading..
+ + +
loading..
- +
- - - - + + + +
- +

Intensity per Cycle - +

- +

Intensity by color and cycle of the 90% percentile of the data for each tile

- - -
loading..
+ + +
loading..
- +
- - - - + + + +
- +

% PF vs % Occupied - +

- +

% Clusters passing filter vs % Wells Occupied

- - -
loading..
+ + +
loading..
- - + +
- - + +
- - + +
- +

@@ -6064,7 +6064,7 @@

MultiQC v1.11.dev0 (d840aff) - Available on GitHub.
Written by Phil Ewels - Modified by Matthias De Smet - +

diff --git a/docs/example/NovaSeq_report.html b/docs/example/NovaSeq_report.html index a466d15..d10dfb3 100644 --- a/docs/example/NovaSeq_report.html +++ b/docs/example/NovaSeq_report.html @@ -12,7 +12,7 @@ http://multiqc.info --> - + @@ -40,7 +40,7 @@ - + @@ -5040,54 +5040,54 @@

- +

Loading report..

@@ -5123,7 +5123,7 @@

Highlight Samples

- +
@@ -5143,7 +5143,7 @@

Rename Samples

- + @@ -5172,7 +5172,7 @@

Show / Hide Samples

- +
@@ -5185,7 +5185,7 @@

- +

Regex mode off @@ -5257,9 +5257,9 @@

Export Plots

- +

Note that additional data was saved in multiqc_data when this report was generated.

- +
@@ -5339,7 +5339,7 @@

About MultiQC

- +

@@ -5377,15 +5377,15 @@

JavaScript Disabled

Report - + generated on 2021-05-21, 16:32 - - + + based on data in: - + /Users/matdsmet/Projects/MultiQC_SAV/test_data/NovaSeq

- - + +
@@ -5398,33 +5398,33 @@

JavaScript Disabled

- - - + + +

Illumina SAV

Illumina SAV - Sequencing Metrics from Illumina sequencers

- - - - + + + +
- +

Run Info - +

- - - - + + + +
- +
@@ -5444,42 +5444,42 @@

Settings

- +
- - - - + + + +
- +

Summary Read Metrics - +

- +

Summary metrics per Read

- - + +
- + - + - + - + Showing 6/6 rows and 6/7 columns. - +
@@ -5511,7 +5511,7 @@

Sav-Read-Metrics-Summary-Table: Columns

- +
|| @@ -5594,42 +5594,42 @@

Sav-Read-Metrics-Summary-Table: Columns

- +
- - - - + + + +
- +

Summary Lane Metrics - +

- +

Summary metrics per Lane per Read

- - + +
- + - + - + - + Showing 16/16 rows and 13/25 columns. - +
@@ -5661,7 +5661,7 @@

Sav-Lane-Metrics-Summary-Table: Columns

- +
|| @@ -5942,26 +5942,26 @@

Sav-Lane-Metrics-Summary-Table: Columns

- +
- - - - + + + +
- +

Clusters/Reads per Lane - +

- +

Total Cluster/Read count per Lane

- - -
- - + + +
+ +
   
@@ -5970,103 +5970,103 @@

loading..

- +
- - - - + + + +
- +

Qscore Heatmap - +

- +

The Qscore Heat Map provides an overview of quality scores across cycles.

- - + +
-
loading..
+
loading..
- +
- - - - + + + +
- +

Qscore Histogram - +

- +

Qscore Histogram graphs the number of bases by quality score. The quality score is cumulative for the current cycle. Only bases from reads that pass the quality filter are included.

- - -
loading..
+ + +
loading..
- +
- - - - + + + +
- +

Intensity per Cycle - +

- +

Intensity by color and cycle of the 90% percentile of the data for each tile

- - -
loading..
+ + +
loading..
- +
- - - - + + + +
- +

% PF vs % Occupied - +

- +

% Clusters passing filter vs % Wells Occupied

- - -
loading..
+ + +
loading..
- - + +
- - + +
- - + +
- +

@@ -6079,7 +6079,7 @@

MultiQC v1.10.1 - Available on GitHub.
Written by Phil Ewels - Modified by Matthias De Smet - +

diff --git a/test_data/HiSeq/RunInfo.xml b/test_data/HiSeq/RunInfo.xml index a99f6d8..b07b9d8 100755 --- a/test_data/HiSeq/RunInfo.xml +++ b/test_data/HiSeq/RunInfo.xml @@ -1,922 +1,922 @@ - - - - HLGNYBBXY - J00178 - 210513 - - - - - - - - 1_1101 - 1_1102 - 1_1103 - 1_1104 - 1_1105 - 1_1106 - 1_1107 - 1_1108 - 1_1109 - 1_1110 - 1_1111 - 1_1112 - 1_1113 - 1_1114 - 1_1115 - 1_1116 - 1_1117 - 1_1118 - 1_1119 - 1_1120 - 1_1121 - 1_1122 - 1_1123 - 1_1124 - 1_1125 - 1_1126 - 1_1127 - 1_1128 - 1_1201 - 1_1202 - 1_1203 - 1_1204 - 1_1205 - 1_1206 - 1_1207 - 1_1208 - 1_1209 - 1_1210 - 1_1211 - 1_1212 - 1_1213 - 1_1214 - 1_1215 - 1_1216 - 1_1217 - 1_1218 - 1_1219 - 1_1220 - 1_1221 - 1_1222 - 1_1223 - 1_1224 - 1_1225 - 1_1226 - 1_1227 - 1_1228 - 1_2101 - 1_2102 - 1_2103 - 1_2104 - 1_2105 - 1_2106 - 1_2107 - 1_2108 - 1_2109 - 1_2110 - 1_2111 - 1_2112 - 1_2113 - 1_2114 - 1_2115 - 1_2116 - 1_2117 - 1_2118 - 1_2119 - 1_2120 - 1_2121 - 1_2122 - 1_2123 - 1_2124 - 1_2125 - 1_2126 - 1_2127 - 1_2128 - 1_2201 - 1_2202 - 1_2203 - 1_2204 - 1_2205 - 1_2206 - 1_2207 - 1_2208 - 1_2209 - 1_2210 - 1_2211 - 1_2212 - 1_2213 - 1_2214 - 1_2215 - 1_2216 - 1_2217 - 1_2218 - 1_2219 - 1_2220 - 1_2221 - 1_2222 - 1_2223 - 1_2224 - 1_2225 - 1_2226 - 1_2227 - 1_2228 - 2_1101 - 2_1102 - 2_1103 - 2_1104 - 2_1105 - 2_1106 - 2_1107 - 2_1108 - 2_1109 - 2_1110 - 2_1111 - 2_1112 - 2_1113 - 2_1114 - 2_1115 - 2_1116 - 2_1117 - 2_1118 - 2_1119 - 2_1120 - 2_1121 - 2_1122 - 2_1123 - 2_1124 - 2_1125 - 2_1126 - 2_1127 - 2_1128 - 2_1201 - 2_1202 - 2_1203 - 2_1204 - 2_1205 - 2_1206 - 2_1207 - 2_1208 - 2_1209 - 2_1210 - 2_1211 - 2_1212 - 2_1213 - 2_1214 - 2_1215 - 2_1216 - 2_1217 - 2_1218 - 2_1219 - 2_1220 - 2_1221 - 2_1222 - 2_1223 - 2_1224 - 2_1225 - 2_1226 - 2_1227 - 2_1228 - 2_2101 - 2_2102 - 2_2103 - 2_2104 - 2_2105 - 2_2106 - 2_2107 - 2_2108 - 2_2109 - 2_2110 - 2_2111 - 2_2112 - 2_2113 - 2_2114 - 2_2115 - 2_2116 - 2_2117 - 2_2118 - 2_2119 - 2_2120 - 2_2121 - 2_2122 - 2_2123 - 2_2124 - 2_2125 - 2_2126 - 2_2127 - 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index 25628ec..c85c863 100755 --- a/test_data/MiSeq/RunCompletionStatus.xml +++ b/test_data/MiSeq/RunCompletionStatus.xml @@ -1,12 +1,12 @@ - - - 1 - SuccessfullyCompleted - 210505_M01101_0075_000000000-JDP9R - 23 - 23 - 318 - 318 - End - None - \ No newline at end of file + + + 1 + SuccessfullyCompleted + 210505_M01101_0075_000000000-JDP9R + 23 + 23 + 318 + 318 + End + None + diff --git a/test_data/MiSeq/RunInfo.xml b/test_data/MiSeq/RunInfo.xml index e28853c..9b2fa8e 100755 --- a/test_data/MiSeq/RunInfo.xml +++ b/test_data/MiSeq/RunInfo.xml @@ -1,15 +1,15 @@ - - - - 000000000-JDP9R - M01101 - 210505 - - - - - - - - - \ No newline at end of file + + + + 000000000-JDP9R + M01101 + 210505 + + + + + + + + + diff --git a/test_data/MiSeq/RunParameters.xml b/test_data/MiSeq/RunParameters.xml index 94e9159..0048801 100755 --- a/test_data/MiSeq/RunParameters.xml +++ b/test_data/MiSeq/RunParameters.xml @@ -1,92 +1,92 @@ - - - MiSeq_1_2 - false - - 000000000-JDP9R - 15028382 - 2022-01-22T00:00:00 - 20513109 - - - MS2862591-00PR2 - 15041807 - 2022-02-01T00:00:00 - 20514492 - - - MS3181617-300V2 - 15033572 - 2022-01-20T00:00:00 - 20521476 - - true - - Post-Run Wash - - true - 4.0.0.1769 - 14 - 1 - 1 - MiSeq Control Software - - 210505_M01101_0075_000000000-JDP9R - M01101 - 75 - 9.5.12 - 4.0.0.1769 - 1.18.54.4 - 000000000-JDP9R - MS2862591-00PR2 - 15033572 - Version2 - MS3181617-300V2 - - - RNASeq_M023 - RNASeq_M023 - Custom - Custom - Amplicon - RNASeq.cmgg@uzgent.be - false - - - - - - - D:\Illumina\MiSeqTemp\210505_M01101_0075_000000000-JDP9R - D:\Illumina\RTATemp\210505_M01101_0075_000000000-JDP9R - D:\Illumina\MiSeqAnalysis\210505_M01101_0075_000000000-JDP9R - 210505 - MissedPostRunWash - C:\ProgramData\Illumina\MiSeq Control Software\Recipe - C:\program files\Illumina\MiSeq Control Software\Recipe - MS3181617-300V2 - D:\Illumina\MiSeq Control Software\SampleSheets - C:\Users\sbsUser\Documents\SampleSheets\RNASeq_sample sheet_M023_stalen 1-8 .csv - D:\Illumina\MiSeq Control Software\Manifests - \\aclfiler.ugent.be\cmgg_upload\MiSeq_M01101\210505_M01101_0075_000000000-JDP9R - AutoFocus - Both - false - true - SampleSheet - 206383205 - 206383205 - RNASeq_M023 - GenerateFastQWorkflow - 3.0.1.49 - 25025 - - - IpdRequested RunMonitoringRequested RunStorageRequested - RNASeq.cmgg@uzgent.be - false - false - false - 17EDC93B463CF8B8 - 25025 - \ No newline at end of file + + + MiSeq_1_2 + false + + 000000000-JDP9R + 15028382 + 2022-01-22T00:00:00 + 20513109 + + + MS2862591-00PR2 + 15041807 + 2022-02-01T00:00:00 + 20514492 + + + MS3181617-300V2 + 15033572 + 2022-01-20T00:00:00 + 20521476 + + true + + Post-Run Wash + + true + 4.0.0.1769 + 14 + 1 + 1 + MiSeq Control Software + + 210505_M01101_0075_000000000-JDP9R + M01101 + 75 + 9.5.12 + 4.0.0.1769 + 1.18.54.4 + 000000000-JDP9R + MS2862591-00PR2 + 15033572 + Version2 + MS3181617-300V2 + + + RNASeq_M023 + RNASeq_M023 + Custom + Custom + Amplicon + RNASeq.cmgg@uzgent.be + false + + + + + + + D:\Illumina\MiSeqTemp\210505_M01101_0075_000000000-JDP9R + D:\Illumina\RTATemp\210505_M01101_0075_000000000-JDP9R + D:\Illumina\MiSeqAnalysis\210505_M01101_0075_000000000-JDP9R + 210505 + MissedPostRunWash + C:\ProgramData\Illumina\MiSeq Control Software\Recipe + C:\program files\Illumina\MiSeq Control Software\Recipe + MS3181617-300V2 + D:\Illumina\MiSeq Control Software\SampleSheets + C:\Users\sbsUser\Documents\SampleSheets\RNASeq_sample sheet_M023_stalen 1-8 .csv + D:\Illumina\MiSeq Control Software\Manifests + \\aclfiler.ugent.be\cmgg_upload\MiSeq_M01101\210505_M01101_0075_000000000-JDP9R + AutoFocus + Both + false + true + SampleSheet + 206383205 + 206383205 + RNASeq_M023 + GenerateFastQWorkflow + 3.0.1.49 + 25025 + + + IpdRequested RunMonitoringRequested RunStorageRequested + RNASeq.cmgg@uzgent.be + false + false + false + 17EDC93B463CF8B8 + 25025 + diff --git a/test_data/NextSeq2000/RunCompletionStatus.xml b/test_data/NextSeq2000/RunCompletionStatus.xml index b53c777..f4d24d5 100755 --- a/test_data/NextSeq2000/RunCompletionStatus.xml +++ b/test_data/NextSeq2000/RunCompletionStatus.xml @@ -4,4 +4,4 @@ false false false - \ No newline at end of file + diff --git a/test_data/NextSeq2000/RunInfo.xml b/test_data/NextSeq2000/RunInfo.xml index bdb17c4..c0e2fa8 100755 --- a/test_data/NextSeq2000/RunInfo.xml +++ b/test_data/NextSeq2000/RunInfo.xml @@ -55,4 +55,3 @@ - diff --git a/test_data/NextSeq2000/RunParameters.xml b/test_data/NextSeq2000/RunParameters.xml index a7b6391..9f4d621 100755 --- a/test_data/NextSeq2000/RunParameters.xml +++ b/test_data/NextSeq2000/RunParameters.xml @@ -56,4 +56,4 @@ None None - \ No newline at end of file + diff --git a/test_data/NextSeq500/RTAConfiguration.xml b/test_data/NextSeq500/RTAConfiguration.xml index 195dc79..b6f2162 100755 --- a/test_data/NextSeq500/RTAConfiguration.xml +++ b/test_data/NextSeq500/RTAConfiguration.xml @@ -1,141 +1,141 @@ - - - - 500000 - 25 - 20 - DataManagerAllInMem - InterOpManagerBase - ThumbnailManager - 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PerformanceDataRunMonitoringAndStorage + NEXTSEQ + true + 76 + 0 + 6 + 6 + false + true + 92 + + + C:\Users\sbsuser\Desktop\Sample sheets OncoRNALab\NSQ_Run936_COPD_146Bcells.csv + diff --git a/test_data/NovaSeq/RunParameters.xml b/test_data/NovaSeq/RunParameters.xml index 6537b5e..01491fb 100755 --- a/test_data/NovaSeq/RunParameters.xml +++ b/test_data/NovaSeq/RunParameters.xml @@ -1,141 +1,141 @@ - - - Both - PairedEnd - A - 151 - 151 - 8 - 8 - 151 - 151 - 8 - 8 - 192 - v3.4.4 - 1.7.5 - NVQ_Run192 - - HW3FGDSXY - 20015843 - 20504473 - 12/11/2021 00:00:00 - 04/29/2021 14:00:00 - 1 - HTWashOnly;S4 - S4 - 1 - 2 - NV0293471-LIB - Universal - 20005221 - 1000008041 - 12/31/2169 00:00:00 - 04/29/2021 14:00:00 - 3 - NV2954072-RGSBS - S4 - 20003250 - 20468436 - 07/27/2021 00:00:00 - 04/29/2021 14:00:00 - 330 - 12 - 330 - 1 - 4 - NV3014609-RGCPE - S4 - 20003249 - 20481683 - 10/07/2021 00:00:00 - 04/29/2021 14:00:00 - 330 - 12 - 5 - NV5116319-BUFFR - S4 - 20003187 - 50000151 - 09/17/2021 00:00:00 - 12 - 04/29/2021 14:00:00 - 3 - - C:\Program Files\Illumina\NovaSeq Control Software\Recipe - - false - /ilmn/outputfolder/210429_A00785_0192_AHW3FGDSXY/ - /ilmn/outputfolder - Z:\outputfolder\210429_A00785_0192_AHW3FGDSXY\ - Y:\210429_A00785_0192_AHW3FGDSXY\ - Y:\ - C:\ProgramData\Illumina\NovaSeq\NovaSeqTemp\210429_A00785_0192_AHW3FGDSXY\ - C:\ProgramData\Illumina\NovaSeq\NovaSeqTemp\RunSetupLogs\A00785_2021-04-29__13_06_03_SideA - 210429 - 210429_A00785_0192_AHW3FGDSXY - true - false - 6764764 - euc1-prod - - true - true - false - false - false - false - false - A00785 - HighThroughput - NovaSeq Control Software - 1.7.5 - 27 - - - Fluidics Board - novaseq_flu@NovaSeq_1.26.1 - - - Left Buffer Interface Board - novaseq_bim@NovaSeq_1.26.1 - - - Right Buffer Interface Board - novaseq_bim@NovaSeq_1.26.1 - - - Chassis Module Board - novaseq_chm@NovaSeq_1.26.1 - - - Camera Interface Board - novaseq_cib_2@NovaSeq_1.26.1 - - - Focus Interface Board - novaseq_fib_2@NovaSeq_1.26.1 - - - Flow Cell Holder Board - novaseq_fch_2@NovaSeq_1.26.1 - - - System Thermal Board - novaseq_syst@NovaSeq_1.26.1 - - - Left Reagent Chiller Board - novaseq_rca@NovaSeq_1.26.1 - - - Right Reagent Chiller Board - novaseq_rca@NovaSeq_1.26.1 - - - true - 17E9048675F6479C - 1.6.3.1575 - Manual - NovaSeqStandard - \ No newline at end of file + + + Both + PairedEnd + A + 151 + 151 + 8 + 8 + 151 + 151 + 8 + 8 + 192 + v3.4.4 + 1.7.5 + NVQ_Run192 + + HW3FGDSXY + 20015843 + 20504473 + 12/11/2021 00:00:00 + 04/29/2021 14:00:00 + 1 + HTWashOnly;S4 + S4 + 1 + 2 + NV0293471-LIB + Universal + 20005221 + 1000008041 + 12/31/2169 00:00:00 + 04/29/2021 14:00:00 + 3 + NV2954072-RGSBS + S4 + 20003250 + 20468436 + 07/27/2021 00:00:00 + 04/29/2021 14:00:00 + 330 + 12 + 330 + 1 + 4 + NV3014609-RGCPE + S4 + 20003249 + 20481683 + 10/07/2021 00:00:00 + 04/29/2021 14:00:00 + 330 + 12 + 5 + NV5116319-BUFFR + S4 + 20003187 + 50000151 + 09/17/2021 00:00:00 + 12 + 04/29/2021 14:00:00 + 3 + + C:\Program Files\Illumina\NovaSeq Control Software\Recipe + + false + /ilmn/outputfolder/210429_A00785_0192_AHW3FGDSXY/ + /ilmn/outputfolder + Z:\outputfolder\210429_A00785_0192_AHW3FGDSXY\ + Y:\210429_A00785_0192_AHW3FGDSXY\ + Y:\ + C:\ProgramData\Illumina\NovaSeq\NovaSeqTemp\210429_A00785_0192_AHW3FGDSXY\ + C:\ProgramData\Illumina\NovaSeq\NovaSeqTemp\RunSetupLogs\A00785_2021-04-29__13_06_03_SideA + 210429 + 210429_A00785_0192_AHW3FGDSXY + true + false + 6764764 + euc1-prod + + true + true + false + false + false + false + false + A00785 + HighThroughput + NovaSeq Control Software + 1.7.5 + 27 + + + Fluidics Board + novaseq_flu@NovaSeq_1.26.1 + + + Left Buffer Interface Board + novaseq_bim@NovaSeq_1.26.1 + + + Right Buffer Interface Board + novaseq_bim@NovaSeq_1.26.1 + + + Chassis Module Board + novaseq_chm@NovaSeq_1.26.1 + + + Camera Interface Board + novaseq_cib_2@NovaSeq_1.26.1 + + + Focus Interface Board + novaseq_fib_2@NovaSeq_1.26.1 + + + Flow Cell Holder Board + novaseq_fch_2@NovaSeq_1.26.1 + + + System Thermal Board + novaseq_syst@NovaSeq_1.26.1 + + + Left Reagent Chiller Board + novaseq_rca@NovaSeq_1.26.1 + + + Right Reagent Chiller Board + novaseq_rca@NovaSeq_1.26.1 + + + true + 17E9048675F6479C + 1.6.3.1575 + Manual + NovaSeqStandard + From dafc01cc28bdb160ccfd2464484789ec71394e8c Mon Sep 17 00:00:00 2001 From: Claude Date: Wed, 17 Dec 2025 09:17:17 +0000 Subject: [PATCH 6/9] ci: add PyPI publish workflow and remove setup.py - Remove setup.py (pyproject.toml handles everything) - Add publish.yaml workflow triggered on GitHub releases - Uses trusted publishing with OIDC (no API tokens needed) --- .github/workflows/publish.yaml | 31 +++++++++++++++++++++++++++++++ setup.py | 5 ----- 2 files changed, 31 insertions(+), 5 deletions(-) create mode 100644 .github/workflows/publish.yaml delete mode 100755 setup.py diff --git a/.github/workflows/publish.yaml b/.github/workflows/publish.yaml new file mode 100644 index 0000000..769d3e1 --- /dev/null +++ b/.github/workflows/publish.yaml @@ -0,0 +1,31 @@ +name: "Publish to PyPI" + +on: + release: + types: [published] + +jobs: + publish: + name: Publish to PyPI + runs-on: ubuntu-latest + environment: pypi + permissions: + id-token: write + + steps: + - name: Checkout code + uses: actions/checkout@v4 + + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version: "3.11" + + - name: Install build dependencies + run: pip install build + + - name: Build package + run: python -m build + + - name: Publish to PyPI + uses: pypa/gh-action-pypi-publish@release/v1 diff --git a/setup.py b/setup.py deleted file mode 100755 index de2040c..0000000 --- a/setup.py +++ /dev/null @@ -1,5 +0,0 @@ -"""Minimal setup.py for backwards compatibility with older pip versions.""" - -from setuptools import setup - -setup() From e033b55d87a7ae32d758a978f813ceaeba9598f9 Mon Sep 17 00:00:00 2001 From: Claude Date: Wed, 17 Dec 2025 09:20:49 +0000 Subject: [PATCH 7/9] fix: exclude test_data from pre-commit file modifications Revert changes to test data XML files and add exclude patterns to prevent pre-commit hooks from modifying test data and example files. --- .pre-commit-config.yaml | 4 + test_data/HiSeq/RunInfo.xml | 1844 +++---- test_data/HiSeq/RunParameters.xml | 250 +- test_data/MiSeq/CompletedJobInfo.xml | 210 +- .../MiSeq/GenerateFASTQRunStatistics.xml | 4726 ++++++++--------- test_data/MiSeq/RunCompletionStatus.xml | 24 +- test_data/MiSeq/RunInfo.xml | 30 +- test_data/MiSeq/RunParameters.xml | 184 +- test_data/NextSeq2000/RunCompletionStatus.xml | 2 +- test_data/NextSeq2000/RunInfo.xml | 1 + test_data/NextSeq2000/RunParameters.xml | 2 +- test_data/NextSeq500/RTAConfiguration.xml | 282 +- test_data/NextSeq500/RunCompletionStatus.xml | 36 +- test_data/NextSeq500/RunInfo.xml | 1776 +++---- test_data/NextSeq500/RunParameters.xml | 1922 +++---- test_data/NovaSeq/RunParameters.xml | 282 +- 16 files changed, 5790 insertions(+), 5785 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 05b5cae..73d112d 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -18,15 +18,19 @@ repos: - id: check-toml - id: debug-statements - id: end-of-file-fixer + exclude: ^(test_data|docs/example)/ - id: trailing-whitespace + exclude: ^(test_data|docs/example)/ - id: mixed-line-ending args: ["--fix=lf"] + exclude: ^(test_data|docs/example)/ # Line ending normalization - repo: https://github.com/Lucas-C/pre-commit-hooks rev: "v1.5.5" hooks: - id: remove-crlf + exclude: ^(test_data|docs/example)/ # Prettier for markdown, yaml, html, json formatting - repo: https://github.com/pre-commit/mirrors-prettier diff --git a/test_data/HiSeq/RunInfo.xml b/test_data/HiSeq/RunInfo.xml index b07b9d8..a99f6d8 100755 --- a/test_data/HiSeq/RunInfo.xml +++ b/test_data/HiSeq/RunInfo.xml @@ -1,922 +1,922 @@ - - - - HLGNYBBXY - J00178 - 210513 - - - - - - - - 1_1101 - 1_1102 - 1_1103 - 1_1104 - 1_1105 - 1_1106 - 1_1107 - 1_1108 - 1_1109 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206670491 + + ManualRunSetup + PerformanceDataRunMonitoringAndStorage + NEXTSEQ + true + 76 + 0 + 6 + 6 + false + true + 92 + + + C:\Users\sbsuser\Desktop\Sample sheets OncoRNALab\NSQ_Run936_COPD_146Bcells.csv + \ No newline at end of file diff --git a/test_data/NovaSeq/RunParameters.xml b/test_data/NovaSeq/RunParameters.xml index 01491fb..6537b5e 100755 --- a/test_data/NovaSeq/RunParameters.xml +++ b/test_data/NovaSeq/RunParameters.xml @@ -1,141 +1,141 @@ - - - Both - PairedEnd - A - 151 - 151 - 8 - 8 - 151 - 151 - 8 - 8 - 192 - v3.4.4 - 1.7.5 - NVQ_Run192 - - HW3FGDSXY - 20015843 - 20504473 - 12/11/2021 00:00:00 - 04/29/2021 14:00:00 - 1 - HTWashOnly;S4 - S4 - 1 - 2 - NV0293471-LIB - Universal - 20005221 - 1000008041 - 12/31/2169 00:00:00 - 04/29/2021 14:00:00 - 3 - NV2954072-RGSBS - S4 - 20003250 - 20468436 - 07/27/2021 00:00:00 - 04/29/2021 14:00:00 - 330 - 12 - 330 - 1 - 4 - NV3014609-RGCPE - S4 - 20003249 - 20481683 - 10/07/2021 00:00:00 - 04/29/2021 14:00:00 - 330 - 12 - 5 - NV5116319-BUFFR - S4 - 20003187 - 50000151 - 09/17/2021 00:00:00 - 12 - 04/29/2021 14:00:00 - 3 - - C:\Program Files\Illumina\NovaSeq Control Software\Recipe - - false - /ilmn/outputfolder/210429_A00785_0192_AHW3FGDSXY/ - /ilmn/outputfolder - Z:\outputfolder\210429_A00785_0192_AHW3FGDSXY\ - Y:\210429_A00785_0192_AHW3FGDSXY\ - Y:\ - C:\ProgramData\Illumina\NovaSeq\NovaSeqTemp\210429_A00785_0192_AHW3FGDSXY\ - C:\ProgramData\Illumina\NovaSeq\NovaSeqTemp\RunSetupLogs\A00785_2021-04-29__13_06_03_SideA - 210429 - 210429_A00785_0192_AHW3FGDSXY - true - false - 6764764 - euc1-prod - - true - true - false - false - false - false - false - A00785 - HighThroughput - NovaSeq Control Software - 1.7.5 - 27 - - - Fluidics Board - novaseq_flu@NovaSeq_1.26.1 - - - Left Buffer Interface Board - novaseq_bim@NovaSeq_1.26.1 - - - Right Buffer Interface Board - novaseq_bim@NovaSeq_1.26.1 - - - Chassis Module Board - novaseq_chm@NovaSeq_1.26.1 - - - Camera Interface Board - novaseq_cib_2@NovaSeq_1.26.1 - - - Focus Interface Board - novaseq_fib_2@NovaSeq_1.26.1 - - - Flow Cell Holder Board - novaseq_fch_2@NovaSeq_1.26.1 - - - System Thermal Board - novaseq_syst@NovaSeq_1.26.1 - - - Left Reagent Chiller Board - novaseq_rca@NovaSeq_1.26.1 - - - Right Reagent Chiller Board - novaseq_rca@NovaSeq_1.26.1 - - - true - 17E9048675F6479C - 1.6.3.1575 - Manual - NovaSeqStandard - + + + Both + PairedEnd + A + 151 + 151 + 8 + 8 + 151 + 151 + 8 + 8 + 192 + v3.4.4 + 1.7.5 + NVQ_Run192 + + HW3FGDSXY + 20015843 + 20504473 + 12/11/2021 00:00:00 + 04/29/2021 14:00:00 + 1 + HTWashOnly;S4 + S4 + 1 + 2 + NV0293471-LIB + Universal + 20005221 + 1000008041 + 12/31/2169 00:00:00 + 04/29/2021 14:00:00 + 3 + NV2954072-RGSBS + S4 + 20003250 + 20468436 + 07/27/2021 00:00:00 + 04/29/2021 14:00:00 + 330 + 12 + 330 + 1 + 4 + NV3014609-RGCPE + S4 + 20003249 + 20481683 + 10/07/2021 00:00:00 + 04/29/2021 14:00:00 + 330 + 12 + 5 + NV5116319-BUFFR + S4 + 20003187 + 50000151 + 09/17/2021 00:00:00 + 12 + 04/29/2021 14:00:00 + 3 + + C:\Program Files\Illumina\NovaSeq Control Software\Recipe + + false + /ilmn/outputfolder/210429_A00785_0192_AHW3FGDSXY/ + /ilmn/outputfolder + Z:\outputfolder\210429_A00785_0192_AHW3FGDSXY\ + Y:\210429_A00785_0192_AHW3FGDSXY\ + Y:\ + C:\ProgramData\Illumina\NovaSeq\NovaSeqTemp\210429_A00785_0192_AHW3FGDSXY\ + C:\ProgramData\Illumina\NovaSeq\NovaSeqTemp\RunSetupLogs\A00785_2021-04-29__13_06_03_SideA + 210429 + 210429_A00785_0192_AHW3FGDSXY + true + false + 6764764 + euc1-prod + + true + true + false + false + false + false + false + A00785 + HighThroughput + NovaSeq Control Software + 1.7.5 + 27 + + + Fluidics Board + novaseq_flu@NovaSeq_1.26.1 + + + Left Buffer Interface Board + novaseq_bim@NovaSeq_1.26.1 + + + Right Buffer Interface Board + novaseq_bim@NovaSeq_1.26.1 + + + Chassis Module Board + novaseq_chm@NovaSeq_1.26.1 + + + Camera Interface Board + novaseq_cib_2@NovaSeq_1.26.1 + + + Focus Interface Board + novaseq_fib_2@NovaSeq_1.26.1 + + + Flow Cell Holder Board + novaseq_fch_2@NovaSeq_1.26.1 + + + System Thermal Board + novaseq_syst@NovaSeq_1.26.1 + + + Left Reagent Chiller Board + novaseq_rca@NovaSeq_1.26.1 + + + Right Reagent Chiller Board + novaseq_rca@NovaSeq_1.26.1 + + + true + 17E9048675F6479C + 1.6.3.1575 + Manual + NovaSeqStandard + \ No newline at end of file From 3f66ec942f84eaa7029047c093de1d270e3d543b Mon Sep 17 00:00:00 2001 From: Claude Date: Wed, 17 Dec 2025 09:21:37 +0000 Subject: [PATCH 8/9] fix: exclude HTML files from prettier Revert docs/example HTML files and remove html from prettier types. --- .pre-commit-config.yaml | 4 +- docs/example/NextSeq500_report.html | 282 +++++++++++++-------------- docs/example/NovaSeq_report.html | 286 ++++++++++++++-------------- 3 files changed, 286 insertions(+), 286 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 73d112d..af1f300 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -32,12 +32,12 @@ repos: - id: remove-crlf exclude: ^(test_data|docs/example)/ - # Prettier for markdown, yaml, html, json formatting + # Prettier for markdown, yaml, json formatting - repo: https://github.com/pre-commit/mirrors-prettier rev: "v3.1.0" hooks: - id: prettier - types_or: [markdown, yaml, html, json] + types_or: [markdown, yaml, json] additional_dependencies: - "prettier@3.1.0" diff --git a/docs/example/NextSeq500_report.html b/docs/example/NextSeq500_report.html index 1e718c6..5db24cb 100644 --- a/docs/example/NextSeq500_report.html +++ b/docs/example/NextSeq500_report.html @@ -12,7 +12,7 @@ http://multiqc.info --> - + @@ -40,7 +40,7 @@ - + @@ -5040,52 +5040,52 @@

- +

Loading report..

@@ -5121,7 +5121,7 @@

Highlight Samples

- +
@@ -5141,7 +5141,7 @@

Rename Samples

- + @@ -5170,7 +5170,7 @@

Show / Hide Samples

- +
@@ -5183,7 +5183,7 @@

- +

Regex mode off @@ -5255,9 +5255,9 @@

Export Plots

- +

Note that additional data was saved in multiqc_data when this report was generated.

- +
@@ -5337,7 +5337,7 @@

About MultiQC

- +

@@ -5375,15 +5375,15 @@

JavaScript Disabled

Report - + generated on 2021-05-18, 09:20 - - + + based on data in: - + /Users/matdsmet/Projects/MultiQC_SAV/test_data/NextSeq500

- - + +
@@ -5396,33 +5396,33 @@

JavaScript Disabled

+ + - - - +

Illumina SAV

Illumina SAV - Sequencing Metrics from Illumina sequencers

- - - - + + + +
- +

Run Info - +

- - - - + + + +
- +
@@ -5442,42 +5442,42 @@

Settings

- +
- - - - + + + +
- +

Summary Read Metrics - +

- +

Summary metrics per Read

- - + +
- + - + - + - + Showing 5/5 rows and 6/7 columns. - +
@@ -5509,7 +5509,7 @@

Sav-Read-Metrics-Summary-Table: Columns

- +
|| @@ -5592,42 +5592,42 @@

Sav-Read-Metrics-Summary-Table: Columns

- +
- - - - + + + +
- +

Summary Lane Metrics - +

- +

Summary metrics per Lane per Read

- - + +
- + - + - + - + Showing 12/12 rows and 13/24 columns. - +
@@ -5659,7 +5659,7 @@

Sav-Lane-Metrics-Summary-Table: Columns

- +
|| @@ -5929,26 +5929,26 @@

Sav-Lane-Metrics-Summary-Table: Columns

- +
- - - - + + + +
- +

Clusters/Reads per Lane - +

- +

Total Cluster/Read count per Lane

- - -
- - + + +
+ +
   
@@ -5957,101 +5957,101 @@

loading..

- +
- - - - + + + +
- +

Qscore Heatmap - +

- +

The Qscore Heat Map provides an overview of quality scores across cycles.

- - + +
-
loading..
+
loading..
- +
- - - - + + + +
- +

Qscore Histogram - +

- +

Qscore Histogram graphs the number of bases by quality score. The quality score is cumulative for the current cycle. Only bases from reads that pass the quality filter are included.

- - -
loading..
+ + +
loading..
- +
- - - - + + + +
- +

Intensity per Cycle - +

- +

Intensity by color and cycle of the 90% percentile of the data for each tile

- - -
loading..
+ + +
loading..
- +
- - - - + + + +
- +

% PF vs % Occupied - +

- +

% Clusters passing filter vs % Wells Occupied

- - -
loading..
+ + +
loading..
- - + +
- - + +
- - + +
- +

@@ -6064,7 +6064,7 @@

MultiQC v1.11.dev0 (d840aff) - Available on GitHub.
Written by Phil Ewels - Modified by Matthias De Smet - +

diff --git a/docs/example/NovaSeq_report.html b/docs/example/NovaSeq_report.html index d10dfb3..a466d15 100644 --- a/docs/example/NovaSeq_report.html +++ b/docs/example/NovaSeq_report.html @@ -12,7 +12,7 @@ http://multiqc.info --> - + @@ -40,7 +40,7 @@ - + @@ -5040,54 +5040,54 @@

- +

Loading report..

@@ -5123,7 +5123,7 @@

Highlight Samples

- +
@@ -5143,7 +5143,7 @@

Rename Samples

- + @@ -5172,7 +5172,7 @@

Show / Hide Samples

- +
@@ -5185,7 +5185,7 @@

- +

Regex mode off @@ -5257,9 +5257,9 @@

Export Plots

- +

Note that additional data was saved in multiqc_data when this report was generated.

- +
@@ -5339,7 +5339,7 @@

About MultiQC

- +

@@ -5377,15 +5377,15 @@

JavaScript Disabled

Report - + generated on 2021-05-21, 16:32 - - + + based on data in: - + /Users/matdsmet/Projects/MultiQC_SAV/test_data/NovaSeq

- - + +
@@ -5398,33 +5398,33 @@

JavaScript Disabled

+ + - - - +

Illumina SAV

Illumina SAV - Sequencing Metrics from Illumina sequencers

- - - - + + + +
- +

Run Info - +

- - - - + + + +
- +
@@ -5444,42 +5444,42 @@

Settings

- +
- - - - + + + +
- +

Summary Read Metrics - +

- +

Summary metrics per Read

- - + +
- + - + - + - + Showing 6/6 rows and 6/7 columns. - +
@@ -5511,7 +5511,7 @@

Sav-Read-Metrics-Summary-Table: Columns

- +
|| @@ -5594,42 +5594,42 @@

Sav-Read-Metrics-Summary-Table: Columns

- +
- - - - + + + +
- +

Summary Lane Metrics - +

- +

Summary metrics per Lane per Read

- - + +
- + - + - + - + Showing 16/16 rows and 13/25 columns. - +
@@ -5661,7 +5661,7 @@

Sav-Lane-Metrics-Summary-Table: Columns

- +
|| @@ -5942,26 +5942,26 @@

Sav-Lane-Metrics-Summary-Table: Columns

- +
- - - - + + + +
- +

Clusters/Reads per Lane - +

- +

Total Cluster/Read count per Lane

- - -
- - + + +
+ +
   
@@ -5970,103 +5970,103 @@

loading..

- +
- - - - + + + +
- +

Qscore Heatmap - +

- +

The Qscore Heat Map provides an overview of quality scores across cycles.

- - + +
-
loading..
+
loading..
- +
- - - - + + + +
- +

Qscore Histogram - +

- +

Qscore Histogram graphs the number of bases by quality score. The quality score is cumulative for the current cycle. Only bases from reads that pass the quality filter are included.

- - -
loading..
+ + +
loading..
- +
- - - - + + + +
- +

Intensity per Cycle - +

- +

Intensity by color and cycle of the 90% percentile of the data for each tile

- - -
loading..
+ + +
loading..
- +
- - - - + + + +
- +

% PF vs % Occupied - +

- +

% Clusters passing filter vs % Wells Occupied

- - -
loading..
+ + +
loading..
- - + +
- - + +
+ - - +
- +

@@ -6079,7 +6079,7 @@

MultiQC v1.10.1 - Available on GitHub.
Written by Phil Ewels - Modified by Matthias De Smet - +

From 6d66bf4122f65fa621ed7e0525f23d0774eb55d4 Mon Sep 17 00:00:00 2001 From: Claude Date: Wed, 17 Dec 2025 09:27:25 +0000 Subject: [PATCH 9/9] ci: add validation to ensure MultiQC reports are generated - Use --strict mode to catch issues - Verify HTML report is generated for each test - Check that SAV module appears in the log file - Output to separate directories per sequencer type --- .github/workflows/linux.yaml | 28 ++++++++++++++++++++++------ 1 file changed, 22 insertions(+), 6 deletions(-) diff --git a/.github/workflows/linux.yaml b/.github/workflows/linux.yaml index 0c1a36f..194ab20 100644 --- a/.github/workflows/linux.yaml +++ b/.github/workflows/linux.yaml @@ -27,22 +27,38 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip setuptools wheel - pip install beautifulsoup4 multiqc + pip install multiqc - name: Install MultiQC_SAV run: pip install . - name: Test MiSeq - run: multiqc -m SAV test_data/MiSeq + run: | + multiqc -m SAV test_data/MiSeq -o test_output/MiSeq --strict + test -f test_output/MiSeq/multiqc_report.html || (echo "ERROR: Report not generated" && exit 1) + test -f test_output/MiSeq/multiqc_data/multiqc.log || (echo "ERROR: Log file missing" && exit 1) + grep -q "SAV" test_output/MiSeq/multiqc_data/multiqc.log || (echo "ERROR: SAV module not found in log" && exit 1) - name: Test HiSeq - run: multiqc -m SAV test_data/HiSeq + run: | + multiqc -m SAV test_data/HiSeq -o test_output/HiSeq --strict + test -f test_output/HiSeq/multiqc_report.html || (echo "ERROR: Report not generated" && exit 1) + grep -q "SAV" test_output/HiSeq/multiqc_data/multiqc.log || (echo "ERROR: SAV module not found in log" && exit 1) - name: Test NextSeq500 - run: multiqc -m SAV test_data/NextSeq500 + run: | + multiqc -m SAV test_data/NextSeq500 -o test_output/NextSeq500 --strict + test -f test_output/NextSeq500/multiqc_report.html || (echo "ERROR: Report not generated" && exit 1) + grep -q "SAV" test_output/NextSeq500/multiqc_data/multiqc.log || (echo "ERROR: SAV module not found in log" && exit 1) - name: Test NextSeq2000 - run: multiqc -m SAV test_data/NextSeq2000 + run: | + multiqc -m SAV test_data/NextSeq2000 -o test_output/NextSeq2000 --strict + test -f test_output/NextSeq2000/multiqc_report.html || (echo "ERROR: Report not generated" && exit 1) + grep -q "SAV" test_output/NextSeq2000/multiqc_data/multiqc.log || (echo "ERROR: SAV module not found in log" && exit 1) - name: Test NovaSeq - run: multiqc -m SAV test_data/NovaSeq + run: | + multiqc -m SAV test_data/NovaSeq -o test_output/NovaSeq --strict + test -f test_output/NovaSeq/multiqc_report.html || (echo "ERROR: Report not generated" && exit 1) + grep -q "SAV" test_output/NovaSeq/multiqc_data/multiqc.log || (echo "ERROR: SAV module not found in log" && exit 1)