Loading zUMIs-master.sh +45 −6 Original line number Diff line number Diff line Loading @@ -2,8 +2,8 @@ # LMU Munich. AG Enard # Pipeline to run UMI-seq analysis from fastq to read count tables. # Authors: Swati Parekh & Christoph Ziegenhain # Contact: parekh@bio.lmu.de or christoph.ziegenhain@ki.se or hellmann@bio.lmu.de vers=0.0.6 # Contact: sparekh@age.mpg.de or christoph.ziegenhain@ki.se or hellmann@bio.lmu.de vers=0.0.6b function check_opts() { value=$1 name=$2 Loading Loading @@ -198,12 +198,51 @@ isstrt=`echo "$isstrt" | tr '[:upper:]' '[:lower:]'` # convert to all lower cas isindrops=`echo "$isindrops" | tr '[:upper:]' '[:lower:]'` # convert to all lower case whichStage=`echo "$whichStage" | tr '[:upper:]' '[:lower:]'` # convert to all lower case memory=`du -sh $genomedir | cut -f1` #STAR genome index size if [[ ! "$outdir" =~ ^[/|~] ]] ; then outdir=`pwd`/$outdir fi if [[ ! "$gtf" =~ ^[/|~] ]] ; then gtf=`pwd`/$gtf fi if [[ ! "$barcodes" =~ ^[/|~|NA|0|1|2|3|4|5|6|7|8|9] ]] ; then barcodes=`pwd`/$barcodes fi if [[ ! "$genomedir" =~ ^[/|~] ]] ; then genomedir=`pwd`/$genomedir fi if [[ ! "$pbcfastq" =~ ^[/|~|NA] ]] ; then pbcfastq=`pwd`/$pbcfastq fi if [[ ! "$bcread2" =~ ^[/|~|NA] ]] ; then bcread2=`pwd`/$bcread2 fi if [[ ! "$libread" =~ ^[/|~|NA] ]] ; then libread=`pwd`/$libread fi if [[ ! "$cdnaread" =~ ^[/|~] ]] ; then cdnaread=`pwd`/$cdnaread fi if [[ ! "$bcread" =~ ^[/|~] ]] ; then bcread=`pwd`/$bcread fi if [[ ! "$CustomMappedBAM" =~ ^[/|~|NA] ]] ; then CustomMappedBAM=`pwd`/$CustomMappedBAM fi memory=`du -sh $genomedir | cut -f1` #STAR genome index size if [[ "$isslurm" != "no" ]] ; then if sinfo; then echo "Your jobs will be submitted to these nodes." Loading Loading
zUMIs-master.sh +45 −6 Original line number Diff line number Diff line Loading @@ -2,8 +2,8 @@ # LMU Munich. AG Enard # Pipeline to run UMI-seq analysis from fastq to read count tables. # Authors: Swati Parekh & Christoph Ziegenhain # Contact: parekh@bio.lmu.de or christoph.ziegenhain@ki.se or hellmann@bio.lmu.de vers=0.0.6 # Contact: sparekh@age.mpg.de or christoph.ziegenhain@ki.se or hellmann@bio.lmu.de vers=0.0.6b function check_opts() { value=$1 name=$2 Loading Loading @@ -198,12 +198,51 @@ isstrt=`echo "$isstrt" | tr '[:upper:]' '[:lower:]'` # convert to all lower cas isindrops=`echo "$isindrops" | tr '[:upper:]' '[:lower:]'` # convert to all lower case whichStage=`echo "$whichStage" | tr '[:upper:]' '[:lower:]'` # convert to all lower case memory=`du -sh $genomedir | cut -f1` #STAR genome index size if [[ ! "$outdir" =~ ^[/|~] ]] ; then outdir=`pwd`/$outdir fi if [[ ! "$gtf" =~ ^[/|~] ]] ; then gtf=`pwd`/$gtf fi if [[ ! "$barcodes" =~ ^[/|~|NA|0|1|2|3|4|5|6|7|8|9] ]] ; then barcodes=`pwd`/$barcodes fi if [[ ! "$genomedir" =~ ^[/|~] ]] ; then genomedir=`pwd`/$genomedir fi if [[ ! "$pbcfastq" =~ ^[/|~|NA] ]] ; then pbcfastq=`pwd`/$pbcfastq fi if [[ ! "$bcread2" =~ ^[/|~|NA] ]] ; then bcread2=`pwd`/$bcread2 fi if [[ ! "$libread" =~ ^[/|~|NA] ]] ; then libread=`pwd`/$libread fi if [[ ! "$cdnaread" =~ ^[/|~] ]] ; then cdnaread=`pwd`/$cdnaread fi if [[ ! "$bcread" =~ ^[/|~] ]] ; then bcread=`pwd`/$bcread fi if [[ ! "$CustomMappedBAM" =~ ^[/|~|NA] ]] ; then CustomMappedBAM=`pwd`/$CustomMappedBAM fi memory=`du -sh $genomedir | cut -f1` #STAR genome index size if [[ "$isslurm" != "no" ]] ; then if sinfo; then echo "Your jobs will be submitted to these nodes." Loading
