smart3 related fixes

zUMIs will try to automatically do this, otherwise convert zUMIs output to loom by simply running `Rscript rds2loom.R myRun.yaml`.

## Changelog

19 July 2020: [zUMIs2.9.3](https://github.com/sdparekh/zUMIs/releases/tag/2.9.3): Add zUMIs version number to header of unmapped bam files. Several bug fixes: prevent error during mapping with memory handling; incorrect Smart-seq3 UMI-fragment counting.

14 July 2020: [zUMIs2.9.2](https://github.com/sdparekh/zUMIs/releases/tag/2.9.2): Several bug fixes: Prevent RAM from ballooning, issues with resuming from different stage. Speed up demultiplexing further by chrosome-wise operations. Remove need for second bam file sorting after hamming collapse by keeping sort order.

10 July 2020: [zUMIs2.9.1](https://github.com/sdparekh/zUMIs/releases/tag/2.9.1): Revert changes from pull request #194 (commit  #ff7e879) that introduced a bug when using PE reads.

  print("Coordinate sorting final bam file...")

  sort_cmd <- paste0(samtoolsexc," sort -O 'BAM' -@ ",opt$num_threads," -m ",mempercpu,"G -o ",sortbamfile," ",outbamfile)

  system(sort_cmd)

  system(paste0("rm ",outbamfile))

}else{

  #run hamming distance collapsing here and write output into bam file

  if(!dir.exists( paste0(opt$out_dir,"/zUMIs_output/molecule_mapping/") )){

}

index_cmd <- paste(samtoolsexc,"index -@",opt$num_threads,sortbamfile)

system(index_cmd)

system(paste0("rm ",outbamfile))

print(Sys.time())

#check if PE / SE flag is set correctly

AllCounts<-readRDS(paste(opt$out_dir,"/zUMIs_output/expression/",opt$project,".dgecounts.rds",sep=""))

featfile_vector <- c(paste0(opt$out_dir,"/",opt$project,".filtered.Aligned.GeneTagged.UBcorrected.sorted.bam"),

                     paste0(opt$out_dir,"/",opt$project,".filtered.Aligned.GeneTagged.sorted.bam"))

featfile <- featfile_vector[which(file.exists(featfile_vector))[1]]

#featfile_vector <- c(paste0(opt$out_dir,"/",opt$project,".filtered.Aligned.GeneTagged.UBcorrected.sorted.bam"),

#                     paste0(opt$out_dir,"/",opt$project,".filtered.Aligned.GeneTagged.sorted.bam"))

#

#featfile <- featfile_vector[which(file.exists(featfile_vector))[1]]

featfile <- paste0(opt$out_dir,"/",opt$project,".filtered.Aligned.GeneTagged.sorted.bam")

#check if PE / SE flag is set correctly

if(is.null(opt$read_layout)){

# 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=2.9.3

vers=2.9.3b

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-------------";