Merge pull request #462 from sjspielman/sjspielman/461-doublet-gha

GHA for doublet-detection module

.github/workflows/run_doublet-detection.yml

@@ -0,0 +1,78 @@
+# This is a workflow to run the doublet-detection module
+# This module has both an renv and a conda environment
+#
+# 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
+
+name: Run doublet-detection analysis module
+env:
+  MODULE_PATH: analyses/doublet-detection
+  AWS_DEFAULT_REGION: us-east-1
+
+concurrency:
+  # only one run per branch at a time
+  group: doublet-detection-${{ github.ref }}
+  cancel-in-progress: true
+
+on:
+  workflow_dispatch:
+  workflow_call:
+  #pull_request:
+  #  branches:
+  #    - main
+  #  paths:
+  #    - analyses/doublet-detection/**
+
+jobs:
+  run-module:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -el {0}
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+
+      # Eventually, a step to download data will go here.
+
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: 4.4.0
+          use-public-rspm: true
+
+      - name: Install dependencies needed to build certain R packages
+        run: |
+          sudo apt-get update
+          # libcurl4-openssl-dev and lzma-dev are needed for Rhtslib, a dependency of scDblFinder:
+          #    https://github.com/samtools/htslib/blob/30c9c50a874059e3dae7ff8c0ad9e8a9258031c8/INSTALL#L31-L41
+          # libglpk-dev is needed for igraph
+          sudo apt-get install \
+            libcurl4-openssl-dev \
+            lzma-dev \
+            libglpk-dev
+
+
+      - 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 }}
+
+      - name: Set up conda
+        uses: conda-incubator/setup-miniconda@v3
+
+      - name: Install conda-lock and activate locked conda environment
+        run: |
+          conda install conda-lock
+          conda-lock install --name test ${MODULE_PATH}/conda-lock.yml
+
+      - name: Run doublet-detection module
+        run: |
+          cd $MODULE_PATH
+          bash run_doublet-detection.sh

analyses/doublet-detection/README.md

@@ -2,7 +2,7 @@
 
 ## Description
 
-This module explores doublet detection across ScPCA datasets.
+This module explores the use of doublet detection methods across ScPCA datasets.
 
 Methods used in this module include the following:
 

analyses/doublet-detection/doublet-detection.Rproj

@@ -0,0 +1,15 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+StripTrailingWhitespace: Yes

analyses/doublet-detection/scripts/00_format-benchmark-data.R

@@ -11,10 +11,9 @@
 #   - In the SCE file, this is in the colData slot
 #   - In the AnnData file, this is in the obs slot
 
-# Load renv
-project_root <- here::here()
+# Load renv environment and libraries
+project_root <- rprojroot::find_root(rprojroot::is_renv_project)
 renv::load(project_root)
-
 library(optparse)
 
 

analyses/doublet-detection/scripts/01a_run-scdblfinder.R

@@ -4,7 +4,7 @@
 
 
 # Load libraries and renv environment ------
-project_root <- here::here()
+project_root <- rprojroot::find_root(rprojroot::is_renv_project)
 renv::load(project_root)
 
 library(SingleCellExperiment)