Merge main into feature/ropenscpca

.github/workflows/docker_cell-type-wilms-tumor-14.yml

@@ -0,0 +1,63 @@
+# This is a workflow to build the docker image for the cell-type-wilms-tumor-14 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-wilms-tumor-14
+
+concurrency:
+  # only one run per branch at a time
+  group: "docker_cell-type-wilms-tumor-14_${{ github.ref }}"
+  cancel-in-progress: true
+
+on:
+  # pull_request:
+  #   branches:
+  #     - main
+  #   paths:
+  #     - "analyses/cell-type-wilms-tumor-14/Dockerfile"
+  #     - "analyses/cell-type-wilms-tumor-14/.dockerignore"
+  #     - "analyses/cell-type-wilms-tumor-14/renv.lock"
+  #     - "analyses/cell-type-wilms-tumor-14/conda-lock.yml"
+  # push:
+  #   branches:
+  #     - main
+  #   paths:
+  #     - "analyses/cell-type-wilms-tumor-14/Dockerfile"
+  #     - "analyses/cell-type-wilms-tumor-14/.dockerignore"
+  #     - "analyses/cell-type-wilms-tumor-14/renv.lock"
+  #     - "analyses/cell-type-wilms-tumor-14/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-wilms-tumor-14"
+          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-wilms-tumor-14"
+      push-ecr: true

.github/workflows/run_cell-type-wilms-tumor-14.yml

@@ -0,0 +1,62 @@
+# This is a workflow to run the cell-type-wilms-tumor-14 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-wilms-tumor-14 analysis module
+env:
+  MODULE_PATH: analyses/cell-type-wilms-tumor-14
+  AWS_DEFAULT_REGION: us-east-2
+
+concurrency:
+  # only one run per branch at a time
+  group: "run_cell-type-wilms-tumor-14_${{ github.ref }}"
+  cancel-in-progress: true
+
+on:
+  workflow_dispatch:
+  # workflow_call:
+  # pull_request:
+  #   branches:
+  #     - main
+  #   paths:
+  #     - analyses/cell-type-wilms-tumor-14/**
+  #     - "!analyses/cell-type-wilms-tumor-14/Dockerfile"
+  #     - "!analyses/cell-type-wilms-tumor-14/.dockerignore"
+  #     - .github/workflows/run_cell-type-wilms-tumor-14.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-wilms-tumor-06/00_run_workflow.R

@@ -59,7 +59,6 @@ for (sample_id in metadata$scpca_sample_id) {
   # create a directory to save the notebooks
   dir.create(file.path(module_base, "notebook", sample_id), showWarnings = FALSE)
 
-
   # Pre-process the data - `Seurat` workflow
   rmarkdown::render(input = file.path(notebook_template_dir, "01_seurat-processing.Rmd"),
                     params = list(scpca_project_id = project_id, sample_id = sample_id),
@@ -81,9 +80,18 @@ for (sample_id in metadata$scpca_sample_id) {
                       output_format = "html_document",
                       output_file = paste0("02b_fetal_kidney_reference_Stewart_", sample_id, ".html"),
                       output_dir = file.path(notebook_output_dir, sample_id))
+
+    # Cluster exploration
+    rmarkdown::render(input = file.path(notebook_template_dir, "03_clustering_exploration.Rmd"),
+                      params = list(scpca_project_id = project_id, sample_id = sample_id),
+                      output_format = "html_document",
+                      output_file = paste0("03_clustering_exploration_", sample_id, ".html"),
+                      output_dir = file.path(notebook_output_dir, sample_id))
 
   }
 }
 
 
 
+
+

analyses/cell-type-wilms-tumor-06/README.md

@@ -151,9 +151,16 @@ The `00_run_workflow.R` contains the following steps:
 
 - loop for each samples:
 
--- `Seurat workflow`, nornalization and clustering: `01_seurat-processing.Rmd` in `notebook_template`
--- `Azimuth` label transfer from the fetal full reference (Cao et al.) in `notebook_template`
--- `Azimuth` label transfer from the fetal kidney reference (Stewart et al.) in `notebook_template`
+  - `Seurat workflow`, normalization and clustering: `01_seurat-processing.Rmd` in `notebook_template`
+
+  - `Azimuth` label transfer from the fetal full reference (Cao et al.): `02a_label-transfer_fetal_full_reference_Cao.Rmd` in `notebook_template`
+
+  - `Azimuth` label transfer from the fetal kidney reference (Stewart et al.): `02b_label-transfer_fetal_kidney_reference_Stewart.Rmd` in `notebook_template`
+
+  - Exploration of clustering, label transfers, marker genes and pathways: `03_clustering_exploration.Rmd` in `notebook_template`
+
+
+For each sample and each of the step, an html report is generated and accessible in the directory `notebook`.
 
 ### Justification 
 
@@ -185,6 +192,7 @@ Here we will use `Azimuth` to transfer labels from the reference.
 We start with the `_process.Rds` data to run `01_seurat-processing.Rmd`. 
 The output of `01_seurat-processing.Rmd` is saved in `results` in a subfolder for each sample and is the input of the second step `02a_label-transfer_fetal_full_reference_Cao.Rmd`.
 The output of `02a_label-transfer_fetal_full_reference_Cao.Rmd` is then the input of `02b_label-transfer_fetal_kidney_reference_Stewart.Rmd`.
+Following the same approach, the output of `02b_label-transfer_fetal_kidney_reference_Stewart.Rmd` is the input of `03_clustering_exploration.Rmd`.
 
 At the end of the workflow, we have a `Seurat`object that contains:
 - normalization and clustering, dimensional reductions

analyses/cell-type-wilms-tumor-06/notebook/README.md

@@ -0,0 +1,29 @@
+# Notebook directory instructions
+
+The notebook directory holds subdirectory for each of the sample in the Wilms tumor dataset SCPCP000006 and the fetal kidney reference that we used for label transfer. 
+
+## Azimuth compatible fetal kidney reference
+
+To perform label transfer using Azimuth and the fetal kidney atlas, a reference is built via [`scripts/download-and-create-fetal-kidney-ref.R`](../scripts/download-and-create-fetal-kidney-ref.R) using the fetal_full.Rds object download from:
+"https://datasets.cellxgene.cziscience.com/40ebb8e4-1a25-4a33-b8ff-02d1156e4e9b.rds"
+
+As part of the `00b_characterize_fetal_kidney_reference_Stewart.Rmd` notebook template, we characterized the fetal kidney reference and generated lists of marker genes for the compartment and cell types composing the reference. 
+
+
+## Analysis per sample
+
+Each of the sample of the Wilms tumor dataset SCPCP000006 as been pre-processed and characterized as the following. 
+Reports for each of the steps are found in the notebook/{sample_id} directory:
+
+- `01_seurat_processing_{sample-id}.html` is the output of the [`01_seurat-processing.Rmd`](../notebook_template/01_seurat-processing.Rmd) notebook template.
+In brief, the `_processed.rds` `sce object` is converted to `Seurat` and normalized using `SCTransform`.
+Dimensionality reduction (`RunPCA` and `RunUMAP`) and clustering (`FindNeighbors` and `FindClusters`) are performed before saving the `Seurat` object. 
+
+- `02a_fetal_full_label-transfer_{sample-id}.html` is the output of the [`02a_label-transfer_fetal_full_reference_Cao.Rmd`](../notebook_template/02a_label-transfer_fetal_full_reference_Cao.Rmd) notebook template.
+In brief, we used `Azimuth` to transfer labels from the `Azimuth` fetal full reference (Cao et al.) 
+
+- `02b_fetal_kidney_label-transfer_{sample-id}.html` is the output of the [`02b_label-transfer_fetal_kidney_reference_Stewart.Rmd`](../notebook_template/02b_label-transfer_fetal_kidney_reference_Stewart.Rmd) notebook template.
+In brief, we used `Azimuth` to transfer labels from the fetal kidney reference (Stewart et al.) 
+
+- `03_clustering_exploration_{sample-id}.html` is the output of the [`03_clustering_exploration.Rmd`](../notebook_template/03_clustering_exploration.Rmd) notebook template.
+In brief, we explore the clustering results, we look into some marker genes, pathways enrichment and label transfer.