corto up and running!

Dockerfile

@@ -7,13 +7,17 @@ RUN apt-get update && apt-get install -y \
     git \
     libcurl4-gnutls-dev \
     libssl-dev \
-    libxml2-dev
+    libxml2-dev \
+    procps  # Adding procps for the 'ps' command
 
 # Install R packages
 RUN Rscript -e "install.packages('remotes', dependencies=TRUE)" \
     && Rscript -e "remotes::install_github('federicogiorgi/corto')"
 
 # Test commands to validate installation
-RUN Rscript -e "library(corto); data('inmat'); print(head(inmat))"
+RUN Rscript -e "library(corto)"
+
+# Clone the corto repository (optional, based on your needs)
+RUN git clone https://github.com/federicogiorgi/corto.git
 
 CMD ["/bin/bash"]

README.md

@@ -15,14 +15,14 @@ Already a pro? Just edit this README.md and make it your own. Want to make it ea
 
 ```
 cd existing_repo
-git remote add origin https://gitlab.com/omic/next/registry/tools/corto.git
+git remote add origin https://gitlab.com/omic/next/registry/tools/clei2block.git
 git branch -M master
 git push -uf origin master
 ```
 
 ## Integrate with your tools
 
-- [ ] [Set up project integrations](https://gitlab.com/omic/next/registry/tools/corto/-/settings/integrations)
+- [ ] [Set up project integrations](https://gitlab.com/omic/next/registry/tools/clei2block/-/settings/integrations)
 
 ## Collaborate with your team
 

main.nf

@@ -0,0 +1,105 @@
+nextflow.enable.dsl=2
+
+process CORTO {
+  container "${params.container}"
+  containerOptions "${params.containerOptions}"
+  publishDir "${params.outdir}/${params.project_name}", mode: 'copy'
+  debug true
+  // maxForks 1
+  stageInMode 'copy'
+
+  input:
+    path gene_expression_matrix
+    path centroid_list
+    path cnv_data // This could be optional
+
+  // Define output channels
+  output:
+    path "regulon.rda", emit: regulon
+    path "*.csv", emit: csv_regulon
+    path "*.log", optional: true, emit: logs // if you have log files
+
+    script:
+    """
+    #!/bin/bash
+
+    # Create an R script
+    cat <<EOF > corto_analysis.R
+    # Print the R version
+    print(R.version.string)
+
+    # Load the corto library
+    library(corto)
+
+    # Function to load data
+    loadData <- function(file_name, expected_var) {
+        load(file_name)
+        if (exists(expected_var)) {
+            data <- get(expected_var)
+        } else {
+            stop(paste("Object", expected_var, "not found in", file_name))
+        }
+        return(data)
+    }
+
+    # Load the input matrix
+    inmat <- loadData("${gene_expression_matrix}", "inmat")
+    print("Dimensions of inmat before any operation:")
+    print(dim(inmat))
+
+    # Load the centroids
+    centroids <- loadData("${centroid_list}", "centroids")
+    print("Length of centroids:")
+    print(length(centroids))
+
+    # Run corto with specified parameters
+    regulon <- corto(inmat, centroids=centroids, nbootstraps=10, p=1e-30, nthreads=2)
+
+    # Save the regulon object for later use
+    save(regulon, file="regulon.rda")
+
+    # Transform regulon into a data frame
+    regulon_to_df <- function(regulon) {
+        result_df <- data.frame(TF = character(),
+                                Target = character(),
+                                TFMode = numeric(),
+                                Likelihood = numeric(),
+                                stringsAsFactors = FALSE)
+
+        for (tf in names(regulon)) {
+            tf_data <- regulon[[tf]]
+            if (is.null(tf_data\$tfmode) || is.null(tf_data\$likelihood)) next
+
+            for (i in seq_along(tf_data\$tfmode)) {
+                tf_mode <- tf_data\$tfmode[[i]]
+                likelihood <- tf_data\$likelihood[[i]]
+                target_name <- names(tf_data\$tfmode)[i]
+                tf_df <- data.frame(TF = tf,
+                                    Target = target_name,
+                                    TFMode = tf_mode,
+                                    Likelihood = likelihood,
+                                    stringsAsFactors = FALSE)
+                result_df <- rbind(result_df, tf_df)
+            }
+        }
+        return(result_df)
+    }
+
+    # Check if regulon is a list and transform it
+    if (is.list(regulon)) {
+        regulon_df <- regulon_to_df(regulon)
+        write.csv(regulon_df, file="regulon.csv", row.names=FALSE)
+    } else {
+        warning("Regulon object is not a list. Custom transformation needed.")
+    }
+
+    EOF
+
+    # Execute the R script
+    Rscript corto_analysis.R
+
+    """
+
+
+
+}

nextflow.config

@@ -0,0 +1,15 @@
+manifest {
+    name                = 'corto'
+    author              = 'omic'
+    recurseSubmodules   = true
+    homePage            = 'https://gitlab.com/omic/next/registry/tools/corto'
+    description         = ''
+    mainScript          = 'main.nf'
+    nextflowVersion     = '!>=21.04.3'
+    defaultBranch       = 'master'
+}
+
+docker {
+    enabled = true
+    temp = 'auto'
+}

test.nf

@@ -0,0 +1,22 @@
+nextflow.enable.dsl=2
+
+// GLOBAL FPSIM2 PARAMS
+params.container = 'corto:latest'
+params.containerOptions = '--gpus all --rm -v /mnt:/mnt'
+params.outdir = '/mnt/OmicNAS/private/old/gabe/corto/outputs'
+params.project_name = 'test'
+
+// // INPUTS
+params.gene_expression_matrix = '/mnt/OmicNAS/private/old/gabe/corto/inputs/inmat.rda'
+params.centroid_list = '/mnt/OmicNAS/private/old/gabe/corto/inputs/centroids.rda'
+params.cnv_data = '/mnt/OmicNAS/private/old/gabe/corto/inputs/cnvmat.rda'
+
+
+include {CORTO} from './main.nf'
+
+workflow {
+  gene_expression_matrix = Channel.fromPath(params.gene_expression_matrix)
+  centroid_list = Channel.fromPath(params.centroid_list)
+  cnv_data = Channel.fromPath(params.cnv_data)
+  CORTO(gene_expression_matrix, centroid_list, cnv_data)
+}