Loading zUMIs-master.sh +7 −4 Original line number Diff line number Diff line Loading @@ -180,6 +180,10 @@ whichStage=`echo "$whichStage" | tr '[:upper:]' '[:lower:]'` # convert to all l memory=`du -sh $genomedir | cut -f1` #STAR genome index size if [[ ! "$o" =~ ^[/|~] ]] ; then o=`pwd`/$o fi if [[ "$isslurm" != "no" ]] ; then if sinfo; then echo "Your jobs will be submitted to these nodes." Loading Loading @@ -322,4 +326,3 @@ if [[ "$isslurm" == "yes" ]] ; then else bash $zumisdir/zUMIs-noslurm.sh $cdnaread $bcread $sname $outdir $xcrange $xmrange $cbasequal $mbasequal $molbcbase $cellbcbase $threads $genomedir $gtf $readlen "$starparams" $starexc $barcodes $strandedness $subsampling $zumisdir $samtoolsexc $isStats $whichStage $bcread2 $BaseTrim $isstrt $xcrange2 $CustomMappedBAM $isCustomFASTQ $nreads $isindrops $libread fi Loading
zUMIs-master.sh +7 −4 Original line number Diff line number Diff line Loading @@ -180,6 +180,10 @@ whichStage=`echo "$whichStage" | tr '[:upper:]' '[:lower:]'` # convert to all l memory=`du -sh $genomedir | cut -f1` #STAR genome index size if [[ ! "$o" =~ ^[/|~] ]] ; then o=`pwd`/$o fi if [[ "$isslurm" != "no" ]] ; then if sinfo; then echo "Your jobs will be submitted to these nodes." Loading Loading @@ -322,4 +326,3 @@ if [[ "$isslurm" == "yes" ]] ; then else bash $zumisdir/zUMIs-noslurm.sh $cdnaread $bcread $sname $outdir $xcrange $xmrange $cbasequal $mbasequal $molbcbase $cellbcbase $threads $genomedir $gtf $readlen "$starparams" $starexc $barcodes $strandedness $subsampling $zumisdir $samtoolsexc $isStats $whichStage $bcread2 $BaseTrim $isstrt $xcrange2 $CustomMappedBAM $isCustomFASTQ $nreads $isindrops $libread fi
