docs: rewrite quantms documentation for DDA-only pipeline

- Completely rewrote usage.md: removed all nf-core RNA-seq boilerplate
  (STAR, fastq columns, genome parameter), replaced with DDA-focused
  content covering SDRF/CSV input, Comet/MS-GF+/Sage search engines,
  MS2PIP+DeepLC+Percolator rescoring, LFQ and TMT/iTRAQ quantification,
  PTM localization, cloud execution, and common parameter combinations
- Rewrote output.md: removed DIA workflow sections, focused on DDA-LFQ
  and DDA-ISO outputs (mzTab, MSstats CSV, parquet PSM tables, pmultiqc);
  added note pointing DIA users to quantmsdiann docs
- Added input.md: new page covering SDRF format (with required/optional
  columns and example), CSV samplesheet, spectra file formats (.raw/.mzML/.d),
  FASTA database recommendations, and TMT correction matrices
- Added publications.md: citations for quantms and all integrated tools
  (Comet, MS-GF+, Sage, MS2PIP, DeepLC, Percolator, MS2Rescore, OpenMS,
  MSstats, pmultiqc, SDRF) plus community/support links
- Updated index.md: added quantms_metro.png workflow diagram and
  updated pipeline overview to include Sage
- Updated mkdocs.yml: expanded nav from 5 to 7 pages (added Input Files
  and Publications), added toc_depth: 2

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: ypriverol

.github/workflows/deploy-docs.yml

@@ -0,0 +1,52 @@
+name: Deploy Documentation
+
+on:
+  push:
+    branches: [gh-pages-source]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Install MkDocs
+        run: pip install mkdocs-material
+
+      - name: Build docs
+        run: mkdocs build --site-dir site
+
+      - name: Setup Pages
+        uses: actions/configure-pages@v5
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: site
+
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.gitignore

@@ -0,0 +1 @@
+.idea

README.md

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+# quantms documentation
+
+This branch contains the MkDocs Material documentation source for quantms.
+
+The documentation is built and deployed to https://docs.quantms.org/ via GitHub Actions.
+
+For the pipeline source code, see the `main` or `dev` branches.

mkdocs.yml

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+site_name: quantms
+docs_dir: mkdocs
+site_description: Cloud-ready Nextflow pipeline for DDA quantitative proteomics
+site_author: BigBio Team
+site_url: https://docs.quantms.org/
+repo_name: bigbio/quantms
+repo_url: https://github.com/bigbio/quantms
+theme:
+  name: material
+  custom_dir: mkdocs/overrides
+  font: false
+  palette:
+    - scheme: default
+      primary: blue
+      accent: indigo
+      toggle:
+        icon: material/brightness-7
+        name: Switch to dark mode
+    - scheme: slate
+      primary: blue
+      accent: indigo
+      toggle:
+        icon: material/brightness-4
+        name: Switch to light mode
+  features:
+    - navigation.sections
+    - navigation.top
+    - navigation.footer
+    - content.code.copy
+extra_css:
+  - https://quantms.org/css/quantms-theme.css
+nav:
+  - Home: index.md
+  - Installation: installation.md
+  - Input Files: input.md
+  - Workflows: workflows.md
+  - Usage: usage.md
+  - Output: output.md
+  - Publications: publications.md
+
+plugins:
+  - search
+
+markdown_extensions:
+  - pymdownx.highlight:
+      anchor_linenums: true
+  - pymdownx.inlinehilite
+  - pymdownx.superfences
+  - pymdownx.tabbed:
+      alternate_style: true
+  - admonition
+  - pymdownx.details
+  - attr_list
+  - tables
+  - toc:
+      permalink: true
+      toc_depth: 2