Update zUMIs-master.sh

isstats=`grep 'make_stats:' $yaml | awk '{print $2}'`

fqfiles=`grep 'name:' $yaml | awk '{print $2}'`

velo=`grep 'velocyto:' $yaml | awk '{print $2}'`

staridxdir=`grep 'STAR_index:' $yaml | awk '{print $2}'`

if grep -q 'samtools_exec:' $yaml

    tar -xj --overwrite -f $miniconda -C $zumisenv

  fi

  #activate zUMIs environment!

  unset PYTHONPATH

  unset PYTHONHOME

  source $zumisenv/bin/activate

  conda-unpack

fi

  exit 1

fi

# Check if the STAR version used for mapping and the one in the provided STAR index are the same

starver=`$starexc --version | sed 's/STAR_//g' | sed 's/\s+//g'`

staridxver=`grep "versionGenome" $staridxdir/genomeParameters.txt | awk '{print $2}' | sed 's/\s+//g'`

if [[ "$starver" != "$staridxver" ]]; then

  echo "WARNING: The STAR version used for mapping is $starver and the STAR index is created using the version $staridxver. This might lead to error while mapping. If you encounter error at the mapping stage, please make sure to create the STAR index using STAR $staridxver."

  #exit 1

fi

#create output folders

outdir=`grep 'out_dir' $yaml | awk '{print $2}'`

#[ -d $outdir ] || mkdir $outdir