Update sncRNA.R

kendomaniac · Oct 4, 2023 · cdf1a76 · cdf1a76
1 parent bad81c1
commit cdf1a76
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/R/sncRNA.R b/R/sncRNA.R
@@ -127,7 +127,7 @@ sncRNA <- function(group=c("sudo", "docker"), fastq.folder=getwd(), scratch.fold
     )
     #calling docker for quantification
     params <- paste(
-        "--cidfile", paste0(fastq.folder, "/dockerID_sncRNA"),
+        "--cidfile", paste0(fastq.folder, "/dockerID"),
         "-v", paste0(scratch.folder, ":/data/scratch"),
         "-v", paste0(ref.folder, ":/data/ref"),
         "-v", paste0(trimmed.dir, ":/data/input"),
@@ -179,14 +179,14 @@ sncRNA <- function(group=c("sudo", "docker"), fastq.folder=getwd(), scratch.fold
   }
 
   #saving log and removing docker container
-  container.id <- readLines(paste(fastq.folder,"/dockerID_sncRNA", sep=""), warn = FALSE)
+  container.id <- readLines(paste(fastq.folder,"/dockerID", sep=""), warn = FALSE)
   system(paste("docker logs ", container.id, " >& ", "sncRNA_",substr(container.id,1,12),".log", sep=""))
   system(paste("docker rm ", container.id, sep=""))
 
   #removing temporary folder
   cat("\n\nRemoving the temporary files ....\n")
 
-  system(paste("rm  -f ",fastq.folder,"/dockerID_sncRNA", sep=""))
+  system(paste("rm  -f ",fastq.folder,"/dockerID", sep=""))
   system(paste("rm  -f ",fastq.folder,"/tempFolderID", sep=""))
 
   system(paste("cp ",paste(path.package(package="docker4seq"),"containers/containers.txt",sep="/")," ",fastq.folder, sep=""))