Mise à jour des scripts R

src/.docker_modules/r-scripts/1.0/HBV_RNAs_count_2.R → src/.docker_modules/r-scripts/1.0/HBV_RNAs_count.R

 #!/bin/Rscript
-# Packages installation
+# Packages loading
 library(ggplot2, quietly = TRUE)
 library(tidyr, quietly = TRUE)
 library(plyr, quietly = TRUE)
@@ -60,7 +60,7 @@ palette_complete <- rbind.data.frame(palette_TSS,
                                      stringsAsFactors = FALSE)
 
 # Load Start_positions_count files:
-identified_SP <- read.table(file = opt$SPvariants[1],
+identified_SP <- read.table(file = opt$SPvariants,
                             header = TRUE)
 
 clean_SP <- identified_SP[!duplicated(identified_SP$id),] %>% 
@@ -108,7 +108,7 @@ ggsave(file = "SP_proportion.png",
        dpi = 300)
 
 # TSS not spliced:
-classified_reads <- read.table(file = opt$classification[1], 
+classified_reads <- read.table(file = opt$classification, 
                                header = TRUE)
 
 not_spliced <- classified_reads[!(classified_reads$read_ID %in% clean_SP$id),]

src/.docker_modules/r-scripts/1.0/Junctions_NanoSplicer_2.R → src/.docker_modules/r-scripts/1.0/Junctions_NanoSplicer.R

@@ -12,19 +12,19 @@ library(optparse)
 
 # Load classification per promoter:
 option_list = list(
-  make_option(c("-c", "--classification"), type="character", default=NULL, 
+  make_option(c("-c", "--classification"), type="character", default="./classification.txt", 
               help="input classification or reads file (.txt)", metavar="character"),
   make_option(c("-j", "--jwr"), type="character", default=NULL, 
               help="input nanosplicer results table (.csv)", metavar="character"))
 opt_parser = OptionParser(option_list=option_list)
 opt = parse_args(opt_parser)
-reads_pos <- read.table(opt$classification[1],
+reads_pos <- read.table(opt$classification,
                         sep = "\t")
 colnames(reads_pos) <- c("id", reads_pos[1,2:length(reads_pos[1,])])
 reads_pos <- reads_pos[2:length(reads_pos$id),]
 
 # Load Nanosplicer results:
-df <- read.csv(opt$jwr[1])
+df <- read.csv(opt$jwr)
 colnames(df)[1] <- "juncNumber"
 
 # split donor and acceptor positions:

src/.docker_modules/r-scripts/1.0/start_positions_individuals_2.R → src/.docker_modules/r-scripts/1.0/Start_positions.R

 #!/bin/Rscript
-# Packages installation
+# Packages loading
 library(dplyr)
 library(ggplot2)
 library(RColorBrewer)
@@ -25,8 +25,8 @@ opt = parse_args(opt_parser)
 #                        pattern="*.txt", 
 #                        all.files=FALSE, 
 #                        full.names=FALSE)
-file_to_load <- opt$input[1]
-splitted <- strsplit(opt$input[1], split = "[/]")[[1]]
+file_to_load <- opt$input
+splitted <- strsplit(opt$input, split = "[/]")[[1]]
 filename <- strsplit(splitted[length(splitted)], split = "[.]")[[1]][1]
 
 sam_bc01 <- read.table(file_to_load, header = F)

src/nf_modules/junction_nanosplicer/main.nf

@@ -11,8 +11,8 @@ process junctions_nanosplicer{
   }
 
   input:
+    path(txt)
     path(csv)
-    path(classification_of_reads_per_RNA)
 
   output:
     path("Rplots.pdf")
@@ -21,6 +21,6 @@ process junctions_nanosplicer{
 
   script:
     """
-    Rscript /Junctions_NanoSplicer/Junctions_NanoSplicer_2.R
+    Rscript Junctions_NanoSplicer.R -c txt -j csv
     """
 }
\ No newline at end of file

src/nf_modules/rna_count/main.nf

+version = "1.0"
+container_url = "xgrand/r-scripts:${version}"
+
+params.rna_count_out = ""
+process rna_count{
+  container = "${container_url}"
+  label "small_mem_mono_cpus"
+  tag "RNA quantification"
+  if (params.rna_count_out != "") {
+    publishDir "results/${params.rna_count_out}", mode: 'copy'
+  }
+
+  input:
+    path(spvariants)
+    path(classification)
+
+  output:
+    path("*.csv")
+    path("*.pdf")
+
+  script:
+    """
+    Rscript HBV_RNAs_count.R -s spvariants -c classification
+    """
+}

src/nf_modules/start_positions/main.nf

@@ -5,7 +5,7 @@ params.start_position_counts_out = ""
 process start_position_individuals{
   container = "${container_url}"
   label "small_mem_mono_cpus"
-  tag "identification de variants d'épissage"
+  tag "start positions"
   if (params.start_position_counts_out != "") {
     publishDir "results/${params.start_position_counts_out}", mode: 'copy'
   }
@@ -20,6 +20,6 @@ process start_position_individuals{
 
   script:
     """
-    Rscript start_positions_individuals.R -i start_position_counts
+    Rscript start_positions.R -i start_position_counts
     """
 }
\ No newline at end of file