Merge branch 'main' into sjspielman/update-analysis-readme

.github/ISSUE_TEMPLATE/create-a-semantic-version-release.md

@@ -23,5 +23,5 @@ If issues must be resolved before creating a release, mark them as blockers in Z
   - Are there any _major_ shifts in project dependencies?
     For example, is there a package that was used throughout Docker environments that has been replaced?
   - Have there been any changes in repo file organization?
-- [ Create a release on GitHub ](https://github.com/AlexsLemonade/OpenScPCA-analysis/releases/new)
+- [ ] [Create a release on GitHub](https://github.com/AlexsLemonade/OpenScPCA-analysis/releases/new)
   - populate the contents with the release notes added to the changelog.

.github/workflows/build-push-docker-module.yml

@@ -20,7 +20,7 @@ permissions:
 jobs:
   build-push:
     name: Build and Push Docker Image
-    if: inputs.push-ecr && github.repository_owner == 'AlexsLemonade'
+    if: github.repository_owner == 'AlexsLemonade'
     environment: prod
     runs-on: openscpca-22.04-big-disk
 
@@ -80,7 +80,7 @@ jobs:
         env:
           DOCKER_BUILD_SUMMARY: false
         with:
-          push: true
+          push: ${{ inputs.push-ecr }}
           context: "{{defaultContext}}:analyses/${{ inputs.module }}"
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}

.github/workflows/docker_all-modules.yml

@@ -69,7 +69,7 @@ jobs:
         if: contains(needs.*.result, 'failure')
         uses: peter-evans/create-issue-from-file@v5
         with:
-          title: Analysis module failing in CI
+          title: Docker image build failing in CI
           content-filepath: |
             .github/cron-issue-templates/all-docker-issue-template.md
           labels: |

.github/workflows/docker_celltype-glioblastoma.yml → .github/workflows/docker_cell-type-glioblastoma.yml

@@ -1,11 +1,11 @@
-# This is a workflow to build the docker image for the celltype-glioblastoma module
+# This is a workflow to build the docker image for the cell-type-glioblastoma 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 celltype-glioblastoma
+name: Build docker image for cell-type-glioblastoma
 
 concurrency:
   # only one run per branch at a time
@@ -17,18 +17,18 @@ on:
   #   branches:
   #     - main
   #   paths:
-  #     - "analyses/celltype-glioblastoma/Dockerfile"
-  #     - "analyses/celltype-glioblastoma/.dockerignore"
-  #     - "analyses/celltype-glioblastoma/renv.lock"
-  #     - "analyses/celltype-glioblastoma/conda-lock.yml"
+  #     - "analyses/cell-type-glioblastoma/Dockerfile"
+  #     - "analyses/cell-type-glioblastoma/.dockerignore"
+  #     - "analyses/cell-type-glioblastoma/renv.lock"
+  #     - "analyses/cell-type-glioblastoma/conda-lock.yml"
   # push:
   #   branches:
   #     - main
   #   paths:
-  #     - "analyses/celltype-glioblastoma/Dockerfile"
-  #     - "analyses/celltype-glioblastoma/.dockerignore"
-  #     - "analyses/celltype-glioblastoma/renv.lock"
-  #     - "analyses/celltype-glioblastoma/conda-lock.yml"
+  #     - "analyses/cell-type-glioblastoma/Dockerfile"
+  #     - "analyses/cell-type-glioblastoma/.dockerignore"
+  #     - "analyses/cell-type-glioblastoma/renv.lock"
+  #     - "analyses/cell-type-glioblastoma/conda-lock.yml"
   workflow_dispatch:
     inputs:
       push-ecr:
@@ -49,7 +49,7 @@ jobs:
       - name: Build image
         uses: docker/build-push-action@v5
         with:
-          context: "{{defaultContext}}:analyses/celltype-glioblastoma"
+          context: "{{defaultContext}}:analyses/cell-type-glioblastoma"
           push: false
           cache-from: type=gha
           cache-to: type=gha,mode=max
@@ -59,5 +59,5 @@ jobs:
     if: github.repository_owner == 'AlexsLemonade' && (github.event_name == 'push' || inputs.push-ecr)
     uses: ./.github/workflows/build-push-docker-module.yml
     with:
-      module: "celltype-glioblastoma"
+      module: "cell-type-glioblastoma"
       push-ecr: true

.github/workflows/run_celltype-glioblastoma.yml → .github/workflows/run_cell-type-glioblastoma.yml

@@ -1,4 +1,4 @@
-# This is a workflow to run the celltype-glioblastoma module
+# This is a workflow to run the cell-type-glioblastoma module
 #
 # Analysis modules are run based on three triggers:
 # - Manual trigger
@@ -7,9 +7,9 @@
 #
 # At initialization, only the manual trigger is active
 
-name: Run celltype-glioblastoma analysis module
+name: Run cell-type-glioblastoma analysis module
 env:
-  MODULE_PATH: analyses/celltype-glioblastoma
+  MODULE_PATH: analyses/cell-type-glioblastoma
   AWS_DEFAULT_REGION: us-east-2
 
 concurrency:
@@ -24,9 +24,9 @@ on:
   #   branches:
   #     - main
   #   paths:
-  #     - analyses/celltype-glioblastoma/**
-  #     - "!analyses/celltype-glioblastoma/Dockerfile"
-  #     - "!analyses/celltype-glioblastoma/.dockerignore"
+  #     - analyses/cell-type-glioblastoma/**
+  #     - "!analyses/cell-type-glioblastoma/Dockerfile"
+  #     - "!analyses/cell-type-glioblastoma/.dockerignore"
   #     - .github/workflows/run_celltype-glioblastoma.yml
 
 jobs:

CHANGELOG.md

@@ -9,6 +9,34 @@ Add new release notes in reverse numerical order (newest first) below this comme
 You may want to add temporary notes here for tracking as features are added, before a new release is ready.
 -->
 
+## v0.2.0
+
+This release adds the first set of community-contributed analyses to the repository.
+These modules are focused on cell type identification and annotation for specific ScPCA datasets.
+Note that many of these modules are still in development at this stage and may not be fully functional.
+
+- `cell-type-dsrct`
+- `cell-type-ETP-ALL-03`
+- `cell-type-glioblastoma`
+- `cell-type-nonETP-ALL-03`
+- `cell-type-wilms-tumor-06`
+- `cell-type-wilms-tumor-14`
+
+
+This release also adds the following new modules developed by the Data Lab:
+
+- `cell-type-consensus`: a module for exploring consensus cell types across multiple annotation methods
+- `hello-clusters`: a demonstration module for clustering analysis using the [`rOpenScPCA` package](https://github.com/AlexsLemonade/rOpenScPCA)
+- `seurat-conversion`: a module for converting `SingleCellExperiment` objects to Seurat objects, also using the `rOpenScPCA` package
+
+Other updates in this release include:
+
+- a new `sync-results.py` script to simplify uploading (and downloading) analysis results from an analysis module to a user's S3 bucket
+- changes from `miniconda` to `miniforge` for conda usage throughout the project
+
+While not part of this repository, we do want to also note that we have created the [`rOpenScPCA` package](https://github.com/AlexsLemonade/rOpenScPCA), which will house utility functions commonly used by analysis modules here.
+The goal is to centralize common functions used across analysis modules to make it easier to share code and maintain consistency across modules.
+
 
 ## v0.1.0
 
@@ -17,7 +45,7 @@ The repository at this stage should be generally complete with respect to infras
 
 With respect to infrastructure, the repository contains the following components:
 
-- detailed documentation in the `docs` directory explaining how to interact with the OpenScPCA project and how to set up and run analyses (published at https://openscpca.readthedocs.io) 
+- detailed documentation in the `docs` directory explaining how to interact with the OpenScPCA project and how to set up and run analyses (published at https://openscpca.readthedocs.io)
 - a `create-analysis-module.py` script for setting up new analysis modules
 - `download-data.py` and `download-results.py` scripts to download data and results from the OpenScPCA project
 - template notebooks, scripts, environment files, and Docker images for analysis modules

analyses/celltype-glioblastoma/environment.yml → analyses/cell-type-glioblastoma/environment.yml

@@ -1,4 +1,4 @@
-name: "openscpca-celltype-glioblastoma"
+name: "openscpca-cell-type-glioblastoma"
 channels:
   - conda-forge
   - bioconda