Modif multi cpus to junction nanosplicer and rebuild docker.

src/.docker_modules/r-bolero/1.2/Junctions_NanoSplicer.R

@@ -8,9 +8,6 @@ library(future, quietly = TRUE)
 library(future.apply)
 library(conflicted, quietly = TRUE)
 
-# Set up parallel processing plan
-plan("multisession", workers = 18)
-
 # Résolution de conflits entre les bibliothèques dplyr et stats
 conflict_prefer("filter", "dplyr")
 conflict_prefer("lag", "dplyr")
@@ -22,9 +19,17 @@ option_list = list(
   make_option(c("-j", "--jwr"), type="character", default=NULL, 
               help="input nanosplicer results table (.csv)", metavar="character"),
   make_option(c("-b", "--barcode"), type="character", default=NULL, 
-              help="input barcode", metavar="character"))
+              help="input barcode", metavar="character"),
+  make_option(c("-t", "--threads"), type = "integer", default = 16,
+              help="Number of threads.")
+)
+
 opt_parser = OptionParser(option_list=option_list)
 opt = parse_args(opt_parser)
+
+# Set up parallel processing plan
+plan("multisession", workers = opt$threads)
+
 reads_pos <- read.table(opt$classification,
                         sep = "\t")
 colnames(reads_pos) <- c("id", reads_pos[1,2:length(reads_pos[1,])])

src/nf_modules/junction_nanosplicer/main.nf

@@ -21,6 +21,6 @@ process junctions_nanosplicer{
     """
     mkdir ${barcode}
     cd ${barcode}/
-    Rscript /Junctions_NanoSplicer.R -c ../${txt} -j ../${csv} -b ${barcode}
+    Rscript /Junctions_NanoSplicer.R -c ../${txt} -j ../${csv} -b ${barcode} --threads ${task.cpus}
     """
 }
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