optimise call to velocyto (011ea0d6) · Commits · github_fork / ZUMIs

runVelocyto.R

+3 −2

Original line number	Diff line number	Diff line
		@@ -28,7 +28,7 @@ featfile <- featfile_vector[which(file.exists(featfile_vector))[1]]
		print(Sys.time())
		#prepare the bam file for use with velocyto
		print("Preparing bam file for velocyto...")
		retag_cmd <- paste0(samtoolsexc," view -@ 2 -h ",featfile," \| sed 's/BC:Z:/CB:Z:/'")
		retag_cmd <- paste0(samtoolsexc," view -@ 2 -h ",featfile," \| sed 's/BC:Z:/CB:Z:/' \| sed 's/GE:Z:/GX:Z:/'")
		velobam <- paste0(opt$out_dir,"/",opt$project,".tagged.forVelocyto.bam")
		#sort_cmd <- paste0(samtoolsexc," sort -m ",mempercpu,"G -O BAM -@ ",opt$num_threads," -o ",velobam )
		out_cmd <- paste0(samtoolsexc," view -b -@ ",opt$num_threads," -o ",velobam," - " )
		@@ -54,6 +54,7 @@ UMI_check <- lapply(opt$sequence_files,
		})

		umi_decision <- ifelse(length(unlist(UMI_check))>0,"","--without-umi")
		mm_decision <- ifelse(opt$counting_opts$primaryHit,"--multimap","")

		#run velocyto

		@@ -62,7 +63,7 @@ velo_check <- suppressWarnings(system("which velocyto",intern =T))
		if(length(velo_check) == 0){
		print("No velocyto installation found in path. Please install it via pip.")
		}else{
		velo_cmd <- paste(velo_check[1],"run -vv -b",bcpath,"-o",paste0(opt$out_dir,"/zUMIs_output/velocity/"),umi_decision, "-e",opt$project,"--samtools-threads",opt$num_threads,"--samtools-memory",mempercpu*1000,velobam,gtf,sep=" ")
		velo_cmd <- paste(velo_check[1],"run -vv --umi-extension Gene -b",bcpath,"-o",paste0(opt$out_dir,"/zUMIs_output/velocity/"),umi_decision,mm_decision, "-e",opt$project,"--samtools-threads",opt$num_threads,"--samtools-memory",mempercpu*1000,velobam,gtf,sep=" ")

		try(system(paste0(velo_cmd," > ",opt$out_dir,"/",opt$project,".velocityo.log.out 2>&1")))
		print("RNA velocity done!")

zUMIs-master.sh

+1 −1

Original line number	Diff line number	Diff line
		@@ -3,7 +3,7 @@
		# Pipeline to run UMI-seq analysis from fastq to read count tables.
		# Authors: Swati Parekh, Christoph Ziegenhain, Beate Vieth & Ines Hellmann
		# Contact: sparekh@age.mpg.de or christoph.ziegenhain@ki.se
		vers=2.7.1b
		vers=2.7.1c
		currentv=`curl -s https://raw.githubusercontent.com/sdparekh/zUMIs/master/zUMIs-master.sh \| grep '^vers=' \| cut -f2 -d "="`
		if [ "$currentv" != "$vers" ]; then echo -e "------------- \n\n Good news! A newer version of zUMIs is available at https://github.com/sdparekh/zUMIs \n\n-------------"; fi

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