Merge pull request #801 from maud-p/05_CopyKAT

Scripts to run `copykat` and `infercnv` for a subselection of Wilms tumor from SCPCP000006
AlexsLemonade · Oct 15, 2024 · ea91b17 · ea91b17
2 parents 571e5ac + c99e1d4
commit ea91b17
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Showing 10 changed files with 987 additions and 73 deletions.
diff --git a/.github/workflows/run_cell-type-wilms-tumor-06.yml b/.github/workflows/run_cell-type-wilms-tumor-06.yml
@@ -49,7 +49,7 @@ jobs:
 
       - name: Install system dependencies
         run: |
-          sudo apt-get install -y libcurl4-openssl-dev libhdf5-dev libglpk40
+          sudo apt-get install -y libcurl4-openssl-dev libhdf5-dev libglpk40 jags
 
       - name: Set up renv
         uses: r-lib/actions/setup-renv@v2

diff --git a/analyses/cell-type-wilms-tumor-06/00_run_workflow.R b/analyses/cell-type-wilms-tumor-06/00_run_workflow.R
@@ -37,6 +37,8 @@ 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 -----------------------------------------
 
@@ -92,10 +94,15 @@ for (sample_id in metadata$scpca_sample_id) {
 }
 
 if (!running_ci) {
+  # 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"),
                     output_format = "html_document",
                     output_file = "04_annotation_Across_Samples_exploration.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")))
+
 }
 
 

diff --git a/analyses/cell-type-wilms-tumor-06/Dockerfile b/analyses/cell-type-wilms-tumor-06/Dockerfile
@@ -16,7 +16,10 @@ ENV OPENSCPCA_DOCKER=TRUE
 ENV RENV_CONFIG_CACHE_ENABLED=FALSE
 
 # Install renv
-RUN R --no-echo --no-restore --no-save -e "install.packages('renv')"
+RUN Rscript -e 'install.packages("renv")'
+
+# Install Rhtslib first to prevent package installation errors
+RUN Rscript -e 'BiocManager::install("Rhtslib")'
 
 # Copy the renv.lock file from the host environment to the image
 COPY renv.lock renv.lock