Merge remote-tracking branch 'origin/main' into UTSouthwesternDSSR/no…

…nETP

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

@@ -13,22 +13,22 @@ concurrency:
   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"
+  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:

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

@@ -64,6 +64,11 @@ jobs:
         with:
           working-directory: ${{ env.MODULE_PATH }}
 
+      - name: Initialize zellkonverter environment
+        run: |
+          cd ${MODULE_PATH}
+          Rscript -e "proc <- basilisk::basiliskStart(env = zellkonverter::zellkonverterAnnDataEnv(), testload = 'anndata'); basilisk::basiliskStop(proc)"
+
       # Update this step as needed to download the desired data
       - name: Download test data and results
         run: |

00_run_workflow.R

@@ -0,0 +1,113 @@
+#!/usr/bin/env Rscript
+
+# USAGE:
+# Rscript 00_run_workflow.R
+#
+# USAGE in CI:
+# Rscript 00_run_workflow.R --testing
+
+# Set up options ----------------------------------------------------------------
+
+library(optparse)
+
+option_list <- list(
+  make_option(
+    opt_str = c("--testing"),
+    type = "logical",
+    default = FALSE,
+    action = "store_true",
+    help = "Use this flag when running on test data"
+  )
+)
+
+opts <- parse_args(OptionParser(option_list = option_list))
+running_ci <- opts$testing
+
+# Run the Label transfer from two fetal references ------------------------------
+
+# get list of samples in the library --------------------------------------------
+root_dir <- rprojroot::find_root(rprojroot::is_git_root)
+project_id <- "SCPCP000006"
+sample_metadata_file <- file.path(root_dir, "data", "current", project_id, "single_cell_metadata.tsv")
+metadata <- read.table(sample_metadata_file, sep = "\t", header = TRUE)
+
+# set path to this module--------------------------------------------------------
+module_base <- file.path(root_dir, "analyses", "cell-type-wilms-tumor-06")
+
+# Download and create the fetal kidney reference (Stewart et al) ----------
+system(command = glue::glue("Rscript ", file.path(module_base,"scripts", "download-and-create-fetal-kidney-ref.R")))
+
+# We build the gene position file reference for infercnv ------------------------
+system(command = glue::glue("Rscript ", file.path(module_base, "scripts", "06a_build-geneposition.R")))
+
+# Characterize the two fetal references -----------------------------------------
+
+# Characterize the fetal full reference (Cao et al.)
+# To be done, next PR
+notebook_template_dir <- file.path(module_base, "notebook_template")
+notebook_output_dir <- file.path(module_base, "notebook")
+# Characterize the fetal kidney reference (Stewart et al.)
+rmarkdown::render(input = file.path(notebook_template_dir, "00b_characterize_fetal_kidney_reference_Stewart.Rmd"),
+                  output_format = "html_document",
+                  output_file = "00b_characterization_fetal_kidney_reference_Stewart.html",
+                  output_dir = file.path(notebook_output_dir, "00-reference"))
+
+
+# Run the workflow for (all) samples in the project -----------------------------
+for (sample_id in metadata$scpca_sample_id) {
+
+  # create a directory to save the pre-processed and labeled `Seurat` objects
+  dir.create(file.path(module_base, "results", sample_id), showWarnings = FALSE)
+  # 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),
+                    output_format = "html_document",
+                    output_file = paste0("01_seurat_processing_", sample_id, ".html"),
+                    output_dir = file.path(notebook_output_dir,  sample_id))
+
+  if (!running_ci) {
+    # Label transfer from the Cao reference using Azimuth
+    rmarkdown::render(input = file.path(notebook_template_dir, "02a_label-transfer_fetal_full_reference_Cao.Rmd"),
+                      params = list(scpca_project_id = project_id, sample_id = sample_id),
+                      output_format = "html_document",
+                      output_file = paste0("02a_fetal_all_reference_Cao_", sample_id, ".html"),
+                      output_dir = file.path(notebook_output_dir, sample_id))
+
+    # Label transfer from the Stewart reference using Seurat
+    rmarkdown::render(input = file.path(notebook_template_dir, "02b_label-transfer_fetal_kidney_reference_Stewart.Rmd"),
+                      params = list(scpca_project_id = project_id, sample_id = 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))
+
+  }
+}
+
+if (!running_ci) {
+  for(thr in c(0.5, 0.75, 0.85, 0.95)){
+  # Run notebook template to explore label transfer and clustering for all samples at once
+  rmarkdown::render(input = file.path(notebook_output_dir, "04_annotation_Across_Samples_exploration.Rmd"),
+                    params = list(mapping_score_thr = thr),
+                    output_format = "html_document",
+                    output_file = glue::glue("04_annotation_Across_Samples_exploration_mappingscore_threshold_",thr,".html"),
+                    output_dir = notebook_output_dir)
+  }
+  # Run infercnv and copykat for a selection of samples
+  system(command = glue::glue("Rscript ", file.path(module_base,"scripts", "explore-cnv-methods.R")))
+
+}
+
+
+
+
+

analyses/cell-type-dsrct/.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-dsrct/cell-type-dsrct.Rproj

@@ -0,0 +1,13 @@
+Version: 1.0
+
+RestoreWorkspace: No
+SaveWorkspace: No
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX