rescue number of star instances from Inf (dc6014ce) · Commits · github_fork / ZUMIs

zUMIs-mapping.R

+7 −0

Original line number	Diff line number	Diff line
		@@ -35,6 +35,12 @@ if(is.na(genome_size)){
		genome_size <- 25 #set average genome size if there was a problem detecting
		}
		num_star_instances <- floor(inp$mem_limit/genome_size)
		if(num_star_instances < 1){
		num_star_instances = 1 #set the number of STAR instances to 1 if it is 0
		}
		if(num_star_instances > inp$num_threads){
		num_star_instances = inp$num_threads
		}

		# GTF file setup ----------------------------------------------------------
		#in case of additional sequences, we need to create a custom GTF
		@@ -100,6 +106,7 @@ if(avail_cores < 2){
		avail_cores = 1
		}


		param_defaults <- paste("--readFilesCommand ",samtools," view -@",samtools_load_cores," --outSAMmultNmax 1 --outFilterMultimapNmax 50 --outSAMunmapped Within --outSAMtype BAM Unsorted --quantMode TranscriptomeSAM")
		param_misc <- paste("--genomeDir",inp$reference$STAR_index,
		"--sjdbGTFfile",gtf_to_use,

+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=2.9.3c
		vers=2.9.3d
		currentv=$(curl -s https://raw.githubusercontent.com/sdparekh/zUMIs/main/zUMIs.sh \| grep '^vers=' \| cut -f2 -d "=")
		if [ "$currentv" != "$vers" ] ; then
		echo -e "------------- \n\n Good news! A newer version of zUMIs is available at https://github.com/sdparekh/zUMIs \n\n-------------";