From cdf1a76d1e10a2cd3f28049c989750beae807fb7 Mon Sep 17 00:00:00 2001 From: giuferrero Date: Wed, 4 Oct 2023 15:29:47 +0200 Subject: [PATCH] Update sncRNA.R --- R/sncRNA.R | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/R/sncRNA.R b/R/sncRNA.R index ab71b9c..54c11f8 100644 --- 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=""))