parallel::mclapply

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

## Changelog

06 May 2022: zUMIs2.9.7b: Update loading reads with RSamtools to avoid version-dependent failure caused by "*" for unmapped reads.

06 May 2022: zUMIs2.9.7b/c: Update loading reads with RSamtools to avoid version-dependent failure caused by "*" for unmapped reads.

16 Jul 2021: zUMIs2.9.7: Change perl [shebang line](https://github.com/sdparekh/zUMIs/issues/261). Change featureCounts settings to assign reads to genes with the longest overlap in case of ambiguous/overlapping annotations. Allow to control the minimum required overlap of reads to genes with a setting `fraction_overlap:` in the counting section.

    taglist <- c(taglist, "GI")

  }

  rsamtools_reads <- mclapply(1:nrow(idxstats), function(x) {

  rsamtools_reads <- parallel::mclapply(1:nrow(idxstats), function(x) {

    if(opt$read_layout == "PE"){

      parms <- ScanBamParam(tag=taglist,

                            what="pos",

# 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=2.9.7b

vers=2.9.7c

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