initial commit

.github/workflows/docker_cell-type-dsrct.yml

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+# This is a workflow to build the docker image for the cell-type-dsrct 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-dsrct
+
+concurrency:
+  # only one run per branch at a time
+  group: "docker_cell-type-dsrct_${{ github.ref }}"
+  cancel-in-progress: true
+
+on:
+  # pull_request:
+  #   branches:
+  #     - main
+  #   paths:
+  #     - "analyses/cell-type-dsrct/Dockerfile"
+  #     - "analyses/cell-type-dsrct/.dockerignore"
+  #     - "analyses/cell-type-dsrct/renv.lock"
+  #     - "analyses/cell-type-dsrct/conda-lock.yml"
+  # push:
+  #   branches:
+  #     - main
+  #   paths:
+  #     - "analyses/cell-type-dsrct/Dockerfile"
+  #     - "analyses/cell-type-dsrct/.dockerignore"
+  #     - "analyses/cell-type-dsrct/renv.lock"
+  #     - "analyses/cell-type-dsrct/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-dsrct"
+          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-dsrct"
+      push-ecr: true

.github/workflows/run_cell-type-dsrct.yml

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+# This is a workflow to run the cell-type-dsrct 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-dsrct analysis module
+env:
+  MODULE_PATH: analyses/cell-type-dsrct
+  AWS_DEFAULT_REGION: us-east-2
+
+concurrency:
+  # only one run per branch at a time
+  group: "run_cell-type-dsrct_${{ github.ref }}"
+  cancel-in-progress: true
+
+on:
+  workflow_dispatch:
+  # workflow_call:
+  # pull_request:
+  #   branches:
+  #     - main
+  #   paths:
+  #     - analyses/cell-type-dsrct/**
+  #     - "!analyses/cell-type-dsrct/Dockerfile"
+  #     - "!analyses/cell-type-dsrct/.dockerignore"
+  #     - .github/workflows/run_cell-type-dsrct.yml
+
+jobs:
+  run-module:
+    if: github.repository_owner == 'AlexsLemonade'
+    runs-on: ubuntu-latest
+
+    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: Set up renv
+        uses: r-lib/actions/setup-renv@v2
+        with:
+          working-directory: ${{ env.MODULE_PATH }}
+
+      # Update this step as needed to download the desired data
+      - name: Download test data
+        run: ./download-data.py --test-data --format SCE
+
+      - name: Run analysis module
+        run: |
+          cd ${MODULE_PATH}
+          # run module script(s) here

analyses/cell-type-dsrct/Dockerfile

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+# A template docker file for creating a new analysis
+FROM ubuntu:22.04
+
+# 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.authors="OpenScPCA [email protected]"
+LABEL org.opencontainers.image.source="https://github.com/AlexsLemonade/OpenScPCA-analysis/tree/main/templates/analysis-module"
+
+# Set an environment variable to allow checking if we are in an OpenScPCA container
+ENV OPENSCPCA_DOCKER=TRUE

analyses/cell-type-dsrct/README.md

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+# DSRCT Cell Type analysis module
+
+
+
+## Description
+
+This analysis aims to annotate the DSRCT samples in the SCPCP000013 (n=7) dataset.
+
+To do so, we will:
+
+- Assess the quality of the data set
+- Curate a list of marker genes associated with DSRCT cells
+- Detect the expression levels of DSRCT marker genes in the data set
+- Identify clusters in the DSRCT samples
+- Use the list of marker genes to identify tumor cells
+- Perform copy number inference to identify tumor cells
+- Annotate normal cells
+- Perform clustering on tumor cells and identify tumor cell states
+
+## Usage
+
+The code for the module will be in the form of a notebook.
+
+## Input files
+
+
+The input is dependent on the output fles run from `download-data.py`. 
+
+```
+./download-data.py --projects SCPCP000013
+```
+
+This downloads the `SingleCellExperiment` files for DSRCT samples.
+
+
+## Output files
+
+Please include a description of the output from your analysis, including:
+
+- Plots from each analysis
+- RDS file containing the processed single cell data set
+
+## Software requirements
+
+The analysis will be done in R using the `Seurat`, `SingleCellExperiment`, and `scran` packages.
+
+## Computational resources
+
+This will be done on a local machine.

analyses/cell-type-dsrct/results/README.md

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+# Results directory instructions
+
+Files in the results directory should not be directly committed to the repository.
+
+Instead, copy results files to an S3 bucket and add a link to the S3 location in this README file.