feat: Add append module for seurat objects

bin/seurat_subset.R → bin/seurat_append_and_subset.R

@@ -16,7 +16,9 @@ option_list <- list(
   make_option(c("-m", "--metadata"), type = "character",
               help = "Metadata with cell status (TME/Malignant)", metavar = "character"),
   make_option(c("-o", "--outdir"), type = "character", default = './',
-              help = "Output directory path", metavar = "character")
+              help = "Output directory path", metavar = "character"),
+  make_option(c("-s", "--subset"), action = "store_true", default = FALSE,
+       help = "Whether to save a subset of the original object")
 )
 
 opt_parser <- OptionParser(option_list = option_list)
@@ -42,11 +44,11 @@ seurat_object <- Seurat::AddMetaData(
   seurat_object, metadata = metadata
   )
 
+if (opt$subset) {
 seurat_object <- subset(
   seurat_object, subset = cell_status == "TME"
 )
-
-#
+}
 
 saveRDS(
   seurat_object, file = file.path(opt$outdir, gsub(".RDS", "_filtered.RDS", basename(opt$file))))

modules/local/helpers/append/main.nf

@@ -0,0 +1,27 @@
+
+process HELPER_SEURAT_APPEND {
+    tag "Adding metadata"
+    label 'process_medium'
+    container 'oandrefonseca/scratch-annotation:main'
+    publishDir "${params.outdir}/data/${task.process}", mode: 'copy', overwrite: true
+
+    input:
+    path seurat_object
+    path metadata
+
+    output:
+    path ("${seurat_object.baseName}_filtered.RDS"), emit: project_rds
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    """
+      seurat_append_and_subset.R -f ${seurat_object} -m ${metadata}
+    """
+
+    stub:
+    """
+      touch ${seurat_object.baseName}_filtered.RDS
+    """
+}

modules/local/helpers/append/meta.yml

@@ -0,0 +1 @@
+// TO BE DONE

modules/local/helpers/subset/resources/usr/bin/seurat_subset.R → modules/local/helpers/append/resources/usr/bin/seurat_append_and_subset.R

@@ -16,7 +16,9 @@ option_list <- list(
   make_option(c("-m", "--metadata"), type = "character",
               help = "Metadata with cell status (TME/Malignant)", metavar = "character"),
   make_option(c("-o", "--outdir"), type = "character", default = './',
-              help = "Output directory path", metavar = "character")
+              help = "Output directory path", metavar = "character"),
+  make_option(c("-s", "--subset"), action = "store_true", default = FALSE,
+       help = "Whether to save a subset of the original object")
 )
 
 opt_parser <- OptionParser(option_list = option_list)
@@ -42,11 +44,11 @@ seurat_object <- Seurat::AddMetaData(
   seurat_object, metadata = metadata
   )
 
+if (opt$subset) {
 seurat_object <- subset(
   seurat_object, subset = cell_status == "TME"
 )
-
-#
+}
 
 saveRDS(
   seurat_object, file = file.path(opt$outdir, gsub(".RDS", "_filtered.RDS", basename(opt$file))))

modules/local/helpers/subset/main.nf

@@ -18,7 +18,7 @@ process HELPER_SEURAT_SUBSET {
 
     script:
         """
-        seurat_subset.R -f ${seurat_object} -m ${cell_malignancy}
+        seurat_append_and_subset.R -f ${seurat_object} -m ${cell_malignancy} --subset
         """
     stub:
         """

modules/local/helpers/subset/resources/usr/bin/seurat_append_and_subset.R

@@ -0,0 +1,54 @@
+#!/usr/bin/env Rscript
+
+library(Seurat)
+library(dplyr)
+library(readr)
+library(tibble)
+library(optparse)
+
+#Sys.setenv(KMP_DUPLICATE_LIB_OK = "TRUE")
+
+#
+
+option_list <- list(
+  make_option(c("-f", "--file"), type = "character", default = NULL,
+              help = "Input dump name", metavar = "character"),
+  make_option(c("-m", "--metadata"), type = "character",
+              help = "Metadata with cell status (TME/Malignant)", metavar = "character"),
+  make_option(c("-o", "--outdir"), type = "character", default = './',
+              help = "Output directory path", metavar = "character"),
+  make_option(c("-s", "--subset"), action = "store_true", default = FALSE,
+       help = "Whether to save a subset of the original object")
+)
+
+opt_parser <- OptionParser(option_list = option_list)
+opt <- parse_args(opt_parser)
+
+#
+
+if (length(opt) == 3) {
+  print_help(opt_parser)
+  stop("At least one argument must be supplied (input file).n", call. = FALSE)
+}
+
+#
+
+seurat_object <- readRDS(file = opt$file)
+metadata <- readr::read_csv(opt$metadata)
+
+metadata <- metadata %>%
+  tibble::column_to_rownames(var = "barcode") %>%
+  as.data.frame()
+
+seurat_object <- Seurat::AddMetaData(
+  seurat_object, metadata = metadata
+  )
+
+if (opt$subset) {
+seurat_object <- subset(
+  seurat_object, subset = cell_status == "TME"
+)
+}
+
+saveRDS(
+  seurat_object, file = file.path(opt$outdir, gsub(".RDS", "_filtered.RDS", basename(opt$file))))