add rectangle to pipeline

docker/environment.yml

@@ -80,6 +80,7 @@ dependencies:
     - pytz==2023.3
     - requests==2.31.0
     - requests-oauthlib==1.3.1
+    - rectanglepy==1.0.0
     - rich==13.3.5
     - rsa==4.9
     - git+https://github.com/omnideconv/scaden.git

docker_rectangle/Dockerfile

@@ -0,0 +1,84 @@
+FROM eddelbuettel/r2u:20.04
+
+LABEL description="Image for Omnideconv benchmarking pipeline"
+LABEL maintainer="Alexander Dietrich"
+
+# needed so that R r-base installation does not get stuck
+ENV DEBIAN_FRONTEND noninteractive
+
+# install system dependencies
+RUN apt-get update -y && apt-get --no-install-recommends --fix-broken install -y git \
+    wget \
+    vim \
+    software-properties-common \
+    dirmngr \
+    gdebi \
+    curl
+
+# install miniconda into /root/miniconda3
+RUN wget \
+    https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
+    && bash Miniconda3-latest-Linux-x86_64.sh -b -p /root/.local/share/r-miniconda \
+    && rm Miniconda3-latest-Linux-x86_64.sh
+
+ENV PATH="/root/.local/share/r-miniconda/bin:${PATH}"
+ARG PATH="/root/.local/share/r-miniconda/bin:${PATH}"
+
+RUN conda --version
+
+RUN conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/main
+RUN conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/r
+
+# create r-omnideconv environment based on yml file
+COPY environment.yml .
+RUN conda env create -f environment.yml
+RUN echo "source activate r-omnideconv" > ~/.bashrc
+
+
+ENV PATH="/root/.local/share/r-miniconda/envs/omnideconv/bin:${PATH}"
+ARG PATH="/root/.local/share/r-miniconda/envs/omnideconv/bin:${PATH}"
+
+# install omnideconv with all dependencies
+RUN apt-get --no-install-recommends --fix-broken install -y libcurl4-openssl-dev \
+    libxml2-dev \
+    libfontconfig1-dev \
+    libssl-dev \
+    libharfbuzz-dev \
+    libfribidi-dev \
+    libfreetype6-dev \
+    libpng-dev \
+    libtiff5-dev \
+    libjpeg-dev \
+    libgdal-dev \
+    cmake
+
+
+RUN R -e "install.packages(c('pak','pkgdepends','devtools','remotes','harmony','terra','igraph', 'RSQLite'), repos='https://cloud.r-project.org')"
+# Note: Set GITHUB_PAT as a build argument if needed: docker build --build-arg GITHUB_PAT=your_token
+RUN R -e "remotes::install_github('omnideconv/omnideconv@benchmark', dependencies = TRUE)"
+#RUN R -e "pak::pkg_install('omnideconv/SCDC')"
+#RUN R -e "pak::pkg_install('omnideconv/SCDC')"
+#RUN R -e "remotes::install_version('NMF', '0.27', repos='https://cloud.r-project.org')"
+
+
+# set systems variable RETICULATE_PYTHON to new conda env, so that omnideconv will use it
+RUN echo "RETICULATE_PYTHON = '/root/.local/share/r-miniconda/envs/r-omnideconv/bin/python'" > /root/.Rprofile
+RUN R -e "reticulate::use_miniconda(condaenv = 'r-omnideconv', required = TRUE)"
+
+# install benchmarking related dependencies
+RUN R -e "install.packages(c('conflicted','docopt','readxl','tidyverse','profvis'), repos='https://cloud.r-project.org')"
+RUN R -e "BiocManager::install('SimBu')"
+
+# install Docker, so that CibersortX can run
+RUN mkdir -p /etc/apt/keyrings
+RUN curl -fsSL https://download.docker.com/linux/ubuntu/gpg | gpg --dearmor -o /etc/apt/keyrings/docker.gpg
+RUN echo \
+  "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.gpg] https://download.docker.com/linux/ubuntu \
+  $(lsb_release -cs) stable" | tee /etc/apt/sources.list.d/docker.list > /dev/null
+RUN apt-get update -y
+RUN apt-get install -y --no-install-recommends \
+    docker-ce \
+    docker-ce-cli \
+    containerd.io
+
+

docker_rectangle/environment.yml

@@ -0,0 +1,6 @@
+name: r-omnideconv
+dependencies:
+  - python=3.11
+  - pip
+  - pip:
+    - rectanglepy==1.0.0

pipeline/bin/computeSignaturesNF.R

@@ -76,7 +76,6 @@ bulk_matrix <- as.matrix(bulk_matrix)
 
 
 
-
 ####################################
 #### Perform signature building ####
 ####################################

pipeline/bin/runDeconvolutionNF.R

@@ -106,6 +106,17 @@ if(method=='cibersortx'){
 #### Perform devonvolution ####
 ###############################
 
+if(method == 'rectangle'){
+  # do not incluce anndata creation in runtime measurement
+  AnnData <- reticulate::import("anndata")
+  counts <- as.data.frame(t(sc_matrix))
+
+  ad <- AnnData$AnnData(X = counts,
+                        obs = data.frame('cell_type' = sc_celltype_annotations, row.names = colnames(sc_matrix)),
+                        var = data.frame('genes' = rownames(sc_matrix), row.names = rownames(sc_matrix)))
+  sc_matrix <- ad 
+}
+
 runtime <- system.time({
 
   deconvolution <- deconvolution_workflow_general(

pipeline/bin/utils.R

@@ -215,6 +215,7 @@ signature_workflow_general <- function(sc_matrix, annotations, annotation_catego
 
   # path to temporary directory that is inside results directory of one unique result 
   tmp_dir_path <- paste0(res_path, '/tmp/')
+  ncores <- as.numeric(ncores)
 
   # Signature building part
   # Dependent on which method we have 
@@ -282,8 +283,7 @@ signature_workflow_general <- function(sc_matrix, annotations, annotation_catego
       model_path = paste0(res_path, '/model'),
       verbose = TRUE
     )
-
-  }else if (method %in% c('autogenes', 'bayesprism', 'bisque', 'music')){
+  } else if (method %in% c('autogenes', 'bayesprism', 'bisque', 'music', 'rectangle')){
     signature <- NULL
 
   } else {
@@ -312,6 +312,7 @@ deconvolution_workflow_general <- function(sc_matrix, annotations, annotation_ca
 
   # path to temporary directory that is inside results directory of one unique result 
   tmp_dir_path <- paste0(res_path, '/tmp/')
+  ncores <- as.numeric(ncores)
 
   if(method=="autogenes"){
 
@@ -463,6 +464,16 @@ deconvolution_workflow_general <- function(sc_matrix, annotations, annotation_ca
     )
     #unlink(tmp_dir_path, recursive=TRUE)
 
+  } else if (method == "rectangle") {
+
+    rp <- reticulate::import("rectanglepy")
+
+    #ad <- anndata::AnnData(X = t(sc_matrix),
+    #                       obs = data.frame('cell_type' = annotations, row.names = colnames(sc_matrix)),
+    #                       var = data.frame('genes' = rownames(sc_matrix), row.names = rownames(sc_matrix)))
+
+    deconvolution <- rp$rectangle(sc_matrix, bulks = as.data.frame(t(bulk_matrix)), n_cpus=ncores)[[1]]
+
   } else {
     message('Selected method is not supported in the benchmark. Please check again.')
     stop()

pipeline/cibersortx_credentials.csv

@@ -1,2 +1,2 @@
 email, token
-alex.dietrich@tum.de,  e1750b96fcfef36421bf9927a9f0fc49
+alex.dietrich@tum.de,   8ad207154371cd524393fd78e1bb16f0

pipeline/main.nf

@@ -118,6 +118,8 @@ process ANALYSIS_SPILLOVER {
 }
 
 process SIMULATE_BULK_UNKNOWN_CELL_TYPE {
+
+      label 'process_default'
 
       publishDir "${params.preProcess_dir}/pseudo_bulk_unknown_content", mode: 'copy'
 
@@ -145,6 +147,8 @@ process SIMULATE_BULK_UNKNOWN_CELL_TYPE {
 
 process ANALYSIS_BULK_UNKNOWN_CELL_TYPE {
 
+      label 'process_default'
+
       input:
       tuple val(sc_dataset), 
             val(sim_bulk_name), 

pipeline/run_cibersortx.sh

@@ -1,3 +1,5 @@
 #!/bin/bash
 
-nextflow -C /nfs/proj/omnideconv_benchmarking/omnideconv/benchmark/pipeline/nextflow_norm.config run /nfs/proj/omnideconv_benchmarking/omnideconv/benchmark/pipeline/main.nf -profile cibersortx -work-dir /localscratch/omnideconv_work "$@"
+nextflow -C /nfs/proj/omnideconv_benchmarking/omnideconv/benchmark/pipeline/nextflow_norm.config run /nfs/proj/omnideconv_benchmarking/omnideconv/benchmark/pipeline/main.nf \
+    -profile cibersortx \
+    -work-dir /localscratch/omnideconv_work "$@"

pipeline/run_default.sh

@@ -1,3 +1,6 @@
 #!/bin/bash
 
-nextflow -C /nfs/proj/omnideconv_benchmarking/omnideconv/benchmark/pipeline/nextflow_norm.config run /nfs/proj/omnideconv_benchmarking/omnideconv/benchmark/pipeline/main.nf -profile apptainer -work-dir /nfs/scratch/nf-core_work/omnideconv.benchmark -with-trace "$@"
+nextflow -C /nfs/proj/omnideconv_benchmarking/omnideconv/benchmark/pipeline/nextflow_norm.config run /nfs/proj/omnideconv_benchmarking/omnideconv/benchmark/pipeline/main.nf \
+ -profile apptainer \
+ -work-dir /nfs/scratch/nf-core_work/omnideconv.benchmark \
+ -with-trace "$@"