Merge branch 'main' into main

.github/workflows/README.md

@@ -19,6 +19,7 @@ It is not meant to be run as a standalone action.
 
 ## Repository maintenance
 
+* `pre-commit.yml` runs pre-commit checks defined by the `.pre-commit-config.yaml` file.
 * `spellcheck.yml` performs spell checking of markdown and R Markdown documents.
 * `code-styling.yml` performs code styling using `styler` and `ruff`.
   * This workflow also consumes `modules_code-styling.txt` to determine which modules to style.

.github/workflows/docker_all-modules.yml

@@ -39,6 +39,9 @@ jobs:
           - cell-type-ewings
           - doublet-detection
           - cell-type-wilms-tumor-06
+          - cell-type-wilms-tumor-14
+          - cell-type-nonETP-ALL-03
+          - cell-type-ETP-ALL-03
     uses: ./.github/workflows/build-push-docker-module.yml
     if: github.repository_owner == 'AlexsLemonade'
     with:

.github/workflows/docker_cell-type-ETP-ALL-03.yml

@@ -0,0 +1,63 @@
+# This is a workflow to build the docker image for the cell-type-ETP-ALL-03 module
+#
+# Docker modules are run on pull requests when code for files that affect the Docker image have changed.
+# If other files are used during the Docker build, they should be added to `paths`
+#
+# At module initialization, this workflow is inactive, and needs to be activated manually
+
+name: Build docker image for cell-type-ETP-ALL-03
+
+concurrency:
+  # only one run per branch at a time
+  group: "docker_cell-type-ETP-ALL-03_${{ github.ref }}"
+  cancel-in-progress: true
+
+on:
+  pull_request:
+    branches:
+      - main
+    paths:
+      - "analyses/cell-type-ETP-ALL-03/Dockerfile"
+      - "analyses/cell-type-ETP-ALL-03/.dockerignore"
+      - "analyses/cell-type-ETP-ALL-03/renv.lock"
+      - "analyses/cell-type-ETP-ALL-03/conda-lock.yml"
+  push:
+    branches:
+      - main
+    paths:
+      - "analyses/cell-type-ETP-ALL-03/Dockerfile"
+      - "analyses/cell-type-ETP-ALL-03/.dockerignore"
+      - "analyses/cell-type-ETP-ALL-03/renv.lock"
+      - "analyses/cell-type-ETP-ALL-03/conda-lock.yml"
+  workflow_dispatch:
+    inputs:
+      push-ecr:
+        description: "Push to AWS ECR"
+        type: boolean
+        required: true
+
+jobs:
+  test-build:
+    name: Test Build Docker Image
+    if: github.event_name == 'pull_request' || (contains(github.event_name, 'workflow_') && !inputs.push-ecr)
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Build image
+        uses: docker/build-push-action@v5
+        with:
+          context: "{{defaultContext}}:analyses/cell-type-ETP-ALL-03"
+          push: false
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+
+  build-push:
+    name: Build and Push Docker Image
+    if: github.repository_owner == 'AlexsLemonade' && (github.event_name == 'push' || inputs.push-ecr)
+    uses: ./.github/workflows/build-push-docker-module.yml
+    with:
+      module: "cell-type-ETP-ALL-03"
+      push-ecr: true

.github/workflows/pre-commit.yml

@@ -0,0 +1,18 @@
+name: Pre-commit check
+on:
+  pull_request:
+    branches:
+      - main
+      - feature/*
+
+jobs:
+  pre-commit:
+    if: github.repository_owner == 'AlexsLemonade'
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+      - uses: pre-commit/[email protected]

.github/workflows/run_all-modules.yml

@@ -34,14 +34,24 @@ jobs:
   cell-type-wilms-14:
     uses: ./.github/workflows/run_cell-type-wilms-tumor-14.yml
 
-  ## Add additional modules above this comment, and to the needs list below
+  cell-type-ETP-ALL-03:
+      uses: ./.github/workflows/run_cell-type-ETP-ALL-03.yml
+
+  cell-type-nonETP-ALL-03:
+      uses: ./.github/workflows/run_cell-type-nonETP-ALL-03.yml
+
+      ## Add additional modules above this comment, and to the needs list below
   check-jobs:
     if: ${{ always() }}
     needs:
       - hello-R
       - hello-python
       - doublet-detection
       - cell-type-ewings
+      - cell-type-wilms-06
+      - cell-type-wilms-14
+      - cell-type-ETP-ALL-03
+      - cell-type-nonETP-ALL-03
     runs-on: ubuntu-latest
     steps:
       - name: Checkout template file

.github/workflows/run_cell-type-ETP-ALL-03.yml

@@ -0,0 +1,92 @@
+# This is a workflow to run the cell-type-ETP-ALL-03 module
+#
+# Analysis modules are run based on three triggers:
+# - Manual trigger
+# - On pull requests where code in the module has changed
+# - As a reusable workflow called from a separate workflow which periodically runs all modules
+#
+# At initialization, only the manual trigger is active
+
+name: Run cell-type-ETP-ALL-03 analysis module
+env:
+  MODULE_PATH: analyses/cell-type-ETP-ALL-03
+  AWS_DEFAULT_REGION: us-east-2
+
+concurrency:
+  # only one run per branch at a time
+  group: "run_cell-type-ETP-ALL-03_${{ github.ref }}"
+  cancel-in-progress: true
+
+on:
+  workflow_dispatch:
+  workflow_call:
+  pull_request:
+    branches:
+      - main
+    paths:
+      - analyses/cell-type-ETP-ALL-03/**
+      - "!analyses/cell-type-ETP-ALL-03/Dockerfile"
+      - "!analyses/cell-type-ETP-ALL-03/.dockerignore"
+      - .github/workflows/run_cell-type-ETP-ALL-03.yml
+
+jobs:
+  run-module:
+    if: github.repository_owner == 'AlexsLemonade'
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -el {0}
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: 4.4.0
+          use-public-rspm: true
+
+      - name: Set up pandoc
+        uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Install system dependencies
+        run: |
+          sudo apt-get install -y libcurl4-openssl-dev \
+            libhdf5-dev \
+            libglpk40 \
+            libxml2-dev \
+            libfontconfig1-dev \
+            libharfbuzz-dev \
+            libfribidi-dev \
+            libtiff5-dev
+
+      - name: Set up renv
+        uses: r-lib/actions/setup-renv@v2
+        with:
+          working-directory: ${{ env.MODULE_PATH }}
+
+      - name: Set up conda
+      # Note that this creates and activates an environment named 'test' by default
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniforge-version: latest
+
+      - name: Install conda-lock and activate locked conda environment
+        run: |
+          conda install conda-lock
+          conda-lock install --name openscpca-cell-type-ETP-ALL-03 ${MODULE_PATH}/conda-lock.yml
+
+      # Update this step as needed to download the desired data
+      - name: Download test data
+        run: |
+          ./download-data.py --projects SCPCP000003 --test-data --format SCE
+          ./download-results.py --projects SCPCP000003 --test-data --modules doublet-detection
+
+      - name: Run analysis module
+        run: |
+          cd ${MODULE_PATH}
+          # run module script(s) here
+          Rscript scripts/00-01_processing_rds.R
+          Rscript scripts/02-03_annotation.R
+          Rscript scripts/multipanel_plot.R

.github/workflows/run_cell-type-wilms-tumor-06.yml

@@ -49,7 +49,7 @@ jobs:
 
       - name: Install system dependencies
         run: |
-          sudo apt-get install -y libcurl4-openssl-dev libhdf5-dev libglpk40
+          sudo apt-get install -y libcurl4-openssl-dev libhdf5-dev libglpk40 jags
 
       - name: Set up renv
         uses: r-lib/actions/setup-renv@v2

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - name: General file size limit
         id: check-added-large-files
@@ -23,7 +23,7 @@ repos:
       - id: check-case-conflict
       - id: check-merge-conflict
   - repo: https://github.com/gitleaks/gitleaks
-    rev: v8.18.4
+    rev: v8.20.1
     hooks:
       - id: gitleaks
   - repo: local

analyses/cell-type-ETP-ALL-03/.Rprofile

@@ -0,0 +1,4 @@
+# Don't activate renv in an OpenScPCA docker image
+if (Sys.getenv('OPENSCPCA_DOCKER') != 'TRUE') {
+  source('renv/activate.R')
+}

analyses/cell-type-ETP-ALL-03/.dockerignore

@@ -0,0 +1,8 @@
+# Ignore everything by default
+*
+
+# Include specific files in the docker environment
+!/renv.lock
+!/requirements.txt
+!/environment.yml
+!/conda-lock.yml

analyses/cell-type-ETP-ALL-03/.gitignore

@@ -0,0 +1,7 @@
+# Results should not be committed
+/results/*
+!/results/README.md
+
+# Ignore the scratch directory (but keep it present)
+/scratch/*
+!/scratch/.gitkeep

analyses/cell-type-ETP-ALL-03/Azimuth_BM_level1.csv

@@ -0,0 +1,18 @@
+tissueType,cellName,ensembl_id_positive_marker,ensembl_id_negative_marker,fullName,ontologyID
+Immune system,B,"ENSG00000163534,ENSG00000132704,ENSG00000012124,ENSG00000138639,ENSG00000153064,ENSG00000156738,ENSG00000116191,ENSG00000104894,ENSG00000133789,ENSG00000105369",,B cell,CL_0000945
+Immune system,CD4 T,"ENSG00000172005,ENSG00000138795,ENSG00000168685,ENSG00000081059,ENSG00000227507,ENSG00000104660,ENSG00000198851,ENSG00000167286,ENSG00000160654,ENSG00000139193",,CD4 T cell,CL_0000624
+Immune system,CD8 T,"ENSG00000172116,ENSG00000153563,ENSG00000184613,ENSG00000167286,ENSG00000198851,ENSG00000160307,ENSG00000100450,ENSG00000160654,ENSG00000227191,ENSG00000271503",,CD8 T cell,CL_0000625
+Immune system,DC,"ENSG00000198178,ENSG00000115718,ENSG00000070031,ENSG00000169432,ENSG00000105251,ENSG00000155367,ENSG00000168913,ENSG00000132514,ENSG00000239961,ENSG00000163687",,Dendritic cell,CL_0000451
+Immune system,HSPC,"ENSG00000172995,ENSG00000186710,ENSG00000101200,ENSG00000163554,ENSG00000119888,ENSG00000188672,ENSG00000131016,ENSG00000112077,ENSG00000172247,ENSG00000170891",,Hematopoietic stem and progenitor cell,CL_0000037
+Immune system,Mono,"ENSG00000197353,ENSG00000110203,ENSG00000166523,ENSG00000104974,ENSG00000158825,ENSG00000162444,ENSG00000186074,ENSG00000171051,ENSG00000125810,ENSG00000014914",,Monocytes,CL_0000576
+Immune system,NK,"ENSG00000189430,ENSG00000198574,ENSG00000134545,ENSG00000150687,ENSG00000117281,ENSG00000156966,ENSG00000100385,ENSG00000115607,ENSG00000143184,ENSG00000150045",,Natural killer cell,CL_0000814
+Immune system,Other T,"ENSG00000144290,ENSG00000111796,ENSG00000168685,ENSG00000215788,ENSG00000069667,ENSG00000107742,ENSG00000178573,ENSG00000113088,ENSG00000152518,ENSG00000145220",,Other T cell,CL_0000084
+Immune system,Macrophage,"ENSG00000166211,ENSG00000121769,ENSG00000073754,ENSG00000275385,ENSG00000159189,ENSG00000173369,ENSG00000170323,ENSG00000173372,ENSG00000130203,ENSG00000250722",,Macrophage,CL_0000235
+Immune system,Early Eryth,"ENSG00000119865,ENSG00000179348,ENSG00000005961,ENSG00000106327,ENSG00000102145,ENSG00000105610,ENSG00000170891,ENSG00000135525,ENSG00000075618,ENSG00000130208",,Early Erythrocyte,CL_0000764
+Immune system,Late Eryth,"ENSG00000196188,ENSG00000112212,ENSG00000204010,ENSG00000188672,ENSG00000112077,ENSG00000163554,ENSG00000075340,ENSG00000119888,ENSG00000213934",,Late Erythrocyte,CL_0000764
+Immune system,Plasma,"ENSG00000115884,ENSG00000222037,ENSG00000211640,ENSG00000048462,ENSG00000211673,ENSG00000240505,ENSG00000211685,ENSG00000167476,ENSG00000143297,ENSG00000243466",,Plasma cell,CL_0000786
+Immune system,Platelet,"ENSG00000150681,ENSG00000187699,ENSG00000088726,ENSG00000169704,ENSG00000163737,ENSG00000163736,ENSG00000153071,ENSG00000113140,ENSG00000176783,ENSG00000124491",,Platelet,CL_0000233
+Immune system,Stromal,"ENSG00000115461,ENSG00000047457,ENSG00000091513,ENSG00000011465,ENSG00000139329,ENSG00000164692,ENSG00000147571,ENSG00000041982,ENSG00000152583,ENSG00000112175",,Stromal cell,CL_0000499
+Immune system,Blast,"ENSG00000002586,ENSG00000173762,ENSG00000124766,ENSG00000177606,ENSG00000117632,ENSG00000123416,ENSG00000167286",,Blast cell,CL_0000055
+Immune system,Cancer,"ENSG00000026508,ENSG00000119888,ENSG00000141736,ENSG00000086205,ENSG00000111057,ENSG00000007062",,Cancer cell,CL_0001064
+Immune system,Pre Eryth,"ENSG00000081237,ENSG00000170180,ENSG00000175792,ENSG00000072274,ENSG00000110195,ENSG00000135218,ENSG00000115232,ENSG00000244734,ENSG00000223609,ENSG00000133742",,Erythroid-like and erythroid precursor cell,CL_0000038

analyses/cell-type-ETP-ALL-03/Dockerfile

@@ -0,0 +1,64 @@
+FROM bioconductor/r-ver:3.19
+
+# Labels following the Open Containers Initiative (OCI) recommendations
+# For more information, see https://specs.opencontainers.org/image-spec/annotations/?v=v1.0.1
+LABEL org.opencontainers.image.title="openscpca/cell-type-ETP-ALL-03"
+LABEL org.opencontainers.image.description="Docker image for the OpenScPCA analysis module 'cell-type-ETP-ALL-03'"
+LABEL org.opencontainers.image.authors="OpenScPCA [email protected]"
+LABEL org.opencontainers.image.source="https://github.com/AlexsLemonade/OpenScPCA-analysis/tree/main/analyses/cell-type-ETP-ALL-03"
+
+# Set an environment variable to allow checking if we are in an OpenScPCA container
+ENV OPENSCPCA_DOCKER=TRUE
+
+# set a name for the conda environment
+ARG ENV_NAME=openscpca-cell-type-ETP-ALL-03
+
+# set environment variables to install conda
+ENV PATH="/opt/conda/bin:${PATH}"
+
+# Install conda via miniforge
+# adapted from https://github.com/conda-forge/miniforge-images/blob/master/ubuntu/Dockerfile
+RUN curl -L "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" -o /tmp/miniforge.sh \
+  && bash /tmp/miniforge.sh -b -p /opt/conda \
+  && rm -f /tmp/miniforge.sh \
+  && conda clean --tarballs --index-cache --packages --yes \
+  && find /opt/conda -follow -type f -name '*.a' -delete \
+  && find /opt/conda -follow -type f -name '*.pyc' -delete \
+  && conda clean --force-pkgs-dirs --all --yes
+
+# Activate conda environments in bash
+RUN ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh \
+  && echo ". /opt/conda/etc/profile.d/conda.sh" >> /etc/skel/.bashrc \
+  && echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc
+
+# Install conda-lock
+RUN conda install --channel=conda-forge --name=base conda-lock \
+  && conda clean --all --yes
+
+# Install renv
+RUN Rscript -e "install.packages('renv')"
+
+# Disable the renv cache to install packages directly into the R library
+ENV RENV_CONFIG_CACHE_ENABLED=FALSE
+
+# Copy conda lock file to image
+COPY conda-lock.yml conda-lock.yml
+
+# restore from conda-lock.yml file and clean up to reduce image size
+RUN conda-lock install -n ${ENV_NAME} conda-lock.yml \
+  && conda clean --all --yes
+
+# Copy the renv.lock file from the host environment to the image
+COPY renv.lock renv.lock
+
+# restore from renv.lock file and clean up to reduce image size
+RUN Rscript -e 'renv::restore()' \
+  && rm -rf ~/.cache/R/renv \
+  && rm -rf /tmp/downloaded_packages \
+  && rm -rf /tmp/Rtmp*
+
+# Activate conda environment on bash launch
+RUN echo "conda activate ${ENV_NAME}" >> ~/.bashrc
+
+# Set CMD to bash to activate the environment when launching
+CMD ["/bin/bash"]