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| Original file line number | Diff line number | Diff line change |
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@@ -28,5 +28,4 @@ demo | |
| # Other things | ||
| .idea | ||
| .vscode | ||
| docs | ||
| test-data | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,91 @@ | ||
| import re | ||
| from pathlib import Path | ||
| import subprocess | ||
| from typing import TypedDict | ||
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| def extract_first_second_level_section(markdown) -> str: | ||
| # Match the first second-level section and capture its content | ||
| pattern = r"(##\s+.*?)(?=(\n##\s+|$))" | ||
| match = re.search(pattern, markdown, re.DOTALL) | ||
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| if not match: | ||
| raise ValueError("Could not find first second-level section in changelog") | ||
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| # Return the matched section | ||
| return match.group(1).strip() | ||
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| class ChangelogData(TypedDict): | ||
| version: str | ||
| url: str | ||
| date: str | ||
| summary: str | ||
| the_rest: str | ||
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| def extract_latest_version(changelog_content) -> ChangelogData: | ||
| """Extract the latest version section from the changelog.""" | ||
| # Skip the first header line | ||
| last_version_changelog = extract_first_second_level_section(changelog_content) | ||
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| # Find the first version section and extract the version, url and date | ||
| matches = re.search(r"^## \[MultiQC v([\d.]+)\]\((.*?)\) - ([\d-]+)", last_version_changelog) | ||
| if not matches: | ||
| raise ValueError("Could not find version information in changelog") | ||
| version, url, date = matches.groups() | ||
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| # Remove the first line | ||
| last_version_changelog = "\n".join(last_version_changelog.splitlines()[1:]).strip() | ||
| # Get data until the third-level header | ||
| next_header_index = last_version_changelog.find("###") | ||
| if next_header_index == -1: | ||
| raise ValueError("Could not find next header in changelog") | ||
| summary = last_version_changelog[:next_header_index].strip() | ||
| the_rest = last_version_changelog[next_header_index:].strip() | ||
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| return {"version": version, "date": date, "url": url, "summary": summary, "the_rest": the_rest} | ||
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| # Read CHANGELOG.md | ||
| changelog_path = Path("CHANGELOG.md") | ||
| if not changelog_path.exists(): | ||
| raise FileNotFoundError("CHANGELOG.md not found") | ||
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| # Create seqeralabs-docs directory if it doesn't exist | ||
| docs_dir = Path("seqeralabs-docs") | ||
| # Clone seqeralabs-docs repo if it doesn't exist | ||
| if not docs_dir.exists(): | ||
| print("Cloning seqeralabs-docs repository...") | ||
| repo_url = "https://github.com/seqeralabs/docs.git" | ||
| try: | ||
| subprocess.run(["git", "clone", repo_url, str(docs_dir)], check=True) | ||
| except subprocess.CalledProcessError as e: | ||
| raise RuntimeError(f"Failed to clone repository: {e}") | ||
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| # Extract latest version | ||
| with open(changelog_path) as f: | ||
| changelog_data: ChangelogData = extract_latest_version(f.read()) | ||
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| # Create output directory | ||
| output_dir = docs_dir / "changelog" / "multiqc" | ||
| output_dir.mkdir(parents=True, exist_ok=True) | ||
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| # Create output file | ||
| mdx_content: str = f"""--- | ||
| title: MultiQC v{changelog_data['version']} | ||
| date: {changelog_data['date']} | ||
| tags: [multiqc] | ||
| --- | ||
| {changelog_data['summary']} | ||
| {{/* truncate */}} | ||
| {changelog_data['the_rest']} | ||
| """ | ||
| with open(output_path := output_dir / f"v{changelog_data['version']}.mdx", "w") as f: | ||
| f.write(mdx_content) | ||
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| # Print version for GitHub Actions | ||
| print(f"::set-output name=version::{changelog_data['version']}") |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,42 @@ | ||
| name: Push changelog to Seqera Docs | ||
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| on: | ||
| release: | ||
| types: [published] | ||
| workflow_dispatch: | ||
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| jobs: | ||
| update-docs: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
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| - name: Clone seqeralabs/docs | ||
| run: | | ||
| git clone https://github.com/seqeralabs/docs.git seqeralabs-docs | ||
| env: | ||
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | ||
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| - name: Set up Python | ||
| uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: "3.x" | ||
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| - name: Convert changelog | ||
| id: convert | ||
| run: python ${GITHUB_WORKSPACE}/.github/workflows/seqera_docs_changelog.py | ||
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| - name: Create Pull Request | ||
| uses: peter-evans/create-pull-request@v5 | ||
| with: | ||
| token: ${{ secrets.SEQERALABS_DOCS }} | ||
| path: seqeralabs-docs | ||
| commit-message: "Changelog: MultiQC ${{ steps.convert.outputs.version }}" | ||
| title: "Changelog: MultiQC ${{ steps.convert.outputs.version }}" | ||
| body: | | ||
| This PR adds the changelog for MultiQC ${{ steps.convert.outputs.version }} to the Seqera documentation. | ||
| This is an automated PR created from the MultiQC repository. | ||
| branch: changelog-multiqc-${{ steps.convert.outputs.version }} | ||
| base: master | ||
| delete-branch: true |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,30 @@ | ||
| --- | ||
| title: Haplocheck | ||
| displayed_sidebar: multiqcSidebar | ||
| description: > | ||
| Haplocheck detects in-sample contamination in mtDNA or WGS sequencing studies by analyzing the mitchondrial content | ||
| --- | ||
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| <!-- | ||
| ~~~~~ DO NOT EDIT ~~~~~ | ||
| This file is autogenerated from the MultiQC module python docstring. | ||
| Do not edit the markdown, it will be overwritten. | ||
| File path for the source of this content: multiqc/modules/haplocheck/haplocheck.py | ||
| ~~~~~~~~~~~~~~~~~~~~~~~ | ||
| --> | ||
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| :::note | ||
| Haplocheck detects in-sample contamination in mtDNA or WGS sequencing studies by analyzing the mitchondrial content | ||
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| [https://github.com/genepi/haplocheck/](https://github.com/genepi/haplocheck/) | ||
| ::: | ||
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| ### File search patterns | ||
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| ```yaml | ||
| haplocheck: | ||
| contents: "\"Sample\"\t\"Contamination Status\"\t\"Contamination Level\"\t\"Distance\"\ | ||
| \t\"Sample Coverage\"" | ||
| num_lines: 10 | ||
| ``` |
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