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Merge pull request #23 from bcbio/deg_qmd
Deg qmd
2 parents 9a8c987 + 2d676bc commit 7cee028

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‎.github/workflows/run_scrna_qc.yml renamed to ‎.github/workflows/01_run_scrna_qc.yml

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‎.github/workflows/run_norm_integration.yml renamed to ‎.github/workflows/02_run_norm_integration.yml

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‎.github/workflows/03_run_scrna_mast.yml

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name: scRNA MAST Analysis
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on:
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push:
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branches: [main]
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paths:
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- '03_differential_expression/scRNA_MAST.qmd'
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pull_request:
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branches: [main]
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paths:
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- '03_differential_expression/scRNA_MAST.qmd'
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workflow_dispatch:
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jobs:
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r-mast:
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runs-on: ubuntu-22.04
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env:
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RENV_PATHS_ROOT: ~/.local/share/renv # persistent cache location
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steps:
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- name: Checkout code
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uses: actions/checkout@v4
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- name: Install pandoc
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run: sudo apt-get update && sudo apt-get install -y pandoc
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- name: Set up R
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uses: r-lib/actions/setup-r@v2
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- name: Install system dependencies for R packages
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run: |
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sudo apt-get update
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sudo apt-get install -y build-essential libcurl4-openssl-dev libssl-dev libxml2-dev libgit2-dev libmagick++-dev libharfbuzz-dev libfribidi-dev libglpk-dev
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shell: bash
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- name: Cache R packages (renv)
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uses: actions/cache@v4
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with:
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path: ${{ env.RENV_PATHS_ROOT }}
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key: ${{ runner.os }}-renv-${{ hashFiles('03_differential_expression/renv.lock') }}
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restore-keys: |
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${{ runner.os }}-renv-
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- name: Set repositories
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run: Rscript ubuntu.R
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- name: Restore environment from renv.lock
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run: |
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install.packages("renv", repos = "https://cloud.r-project.org")
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renv::restore(prompt = FALSE, lockfile = "03_differential_expression/renv.lock")
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shell: Rscript {0}
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- name: Run MAST analysis for cluster 2
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run: |
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cd 03_differential_expression
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Rscript MAST_analysis.R \
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--seurat_obj=https://github.com/bcbio/bcbioR-test-data/raw/refs/heads/main/singlecell/tiny.rds \
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--resolution_column=integrated_snn_res.0.4 \
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--cluster_name=2 \
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--contrast=age \
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--outputDir=out
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shell: bash
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- name: Set up Quarto
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uses: quarto-dev/quarto-actions/setup@v2
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- name: Run MAST analysis
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id: render_qmd
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run: |
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cd 03_differential_expression
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quarto render scRNA_MAST.qmd
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shell: bash
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- name: Deploy HTML to gh-pages
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if: success()
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run: |
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git config --global user.name "github-actions[bot]"
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git config --global user.email "github-actions[bot]@users.noreply.github.com"
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OUTPUT_FILE="03_differential_expression/scRNA_MAST.html"
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# Fetch gh-pages (if exists) and create worktree
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git fetch origin gh-pages || true
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git worktree add /tmp/gh-pages gh-pages 2>/dev/null || git worktree add /tmp/gh-pages -b gh-pages
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# Copy the file into the worktree
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mkdir -p "/tmp/gh-pages/$(dirname "$OUTPUT_FILE")"
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cp "$OUTPUT_FILE" "/tmp/gh-pages/$(dirname "$OUTPUT_FILE")/"
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cd /tmp/gh-pages
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# Commit and push if there are changes
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git add "$(dirname "$OUTPUT_FILE")/$(basename "$OUTPUT_FILE")"
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git commit -m "Deploy $(basename "$OUTPUT_FILE") [skip ci]"
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git push --force origin gh-pages
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shell: bash

‎.github/workflows/03_run_scrna_pseudobulk.yml

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name: scRNA Pseudobulk Analysis
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on:
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push:
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branches: [main]
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paths:
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- '03_differential_expression/scRNA_pseudobulk.qmd'
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pull_request:
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branches: [main]
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paths:
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- '03_differential_expression/scRNA_pseudobulk.qmd'
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workflow_dispatch:
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jobs:
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r-pseudobulk:
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runs-on: ubuntu-22.04
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env:
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RENV_PATHS_ROOT: ~/.local/share/renv # persistent cache location
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steps:
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- name: Checkout code
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uses: actions/checkout@v4
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- name: Install pandoc
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run: sudo apt-get update && sudo apt-get install -y pandoc
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- name: Set up R
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uses: r-lib/actions/setup-r@v2
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- name: Install system dependencies for R packages
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run: |
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sudo apt-get update
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sudo apt-get install -y build-essential libcurl4-openssl-dev libssl-dev libxml2-dev libgit2-dev libmagick++-dev libharfbuzz-dev libfribidi-dev libglpk-dev
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shell: bash
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- name: Cache R packages (renv)
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uses: actions/cache@v4
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with:
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path: ${{ env.RENV_PATHS_ROOT }}
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key: ${{ runner.os }}-renv-${{ hashFiles('03_differential_expression/renv.lock') }}
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restore-keys: |
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${{ runner.os }}-renv-
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- name: Set repositories
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run: Rscript ubuntu.R
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- name: Restore environment from renv.lock
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run: |
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install.packages("renv", repos = "https://cloud.r-project.org")
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renv::restore(prompt = FALSE, lockfile = "03_differential_expression/renv.lock")
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shell: Rscript {0}
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- name: Set up Quarto
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uses: quarto-dev/quarto-actions/setup@v2
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- name: Run pseudobulk analysis
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id: render_qmd
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run: |
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cd 03_differential_expression
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quarto render scRNA_pseudobulk.qmd
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shell: bash
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- name: Deploy HTML to gh-pages
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if: success()
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run: |
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git config --global user.name "github-actions[bot]"
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git config --global user.email "github-actions[bot]@users.noreply.github.com"
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OUTPUT_FILE="03_differential_expression/scRNA_pseudobulk.html"
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# Fetch gh-pages (if exists) and create worktree
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git fetch origin gh-pages || true
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git worktree add /tmp/gh-pages gh-pages 2>/dev/null || git worktree add /tmp/gh-pages -b gh-pages
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# Copy the file into the worktree
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mkdir -p "/tmp/gh-pages/$(dirname "$OUTPUT_FILE")"
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cp "$OUTPUT_FILE" "/tmp/gh-pages/$(dirname "$OUTPUT_FILE")/"
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cd /tmp/gh-pages
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# Commit and push if there are changes
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git add "$(dirname "$OUTPUT_FILE")/$(basename "$OUTPUT_FILE")"
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git commit -m "Deploy $(basename "$OUTPUT_FILE") [skip ci]"
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git push --force origin gh-pages
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shell: bash

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