Merge branch 'master' of dgt-gitlab.gsc.riken.jp:tom/cellranger_convert into kai

	    echo "  total of $lock cellranger ${cellrangerversion} jobs are already running in ${cellrangerpath} with barcode length (${lastcall_b}), UMI length (${lastcall_u}), and whitelist barcodes (${lastcall_p})"

	    #check if a custom barcode is used for a run (which cannot be run in parallel)

            currentbarcode=$(echo $barcodefile | rev | cut -d"/" -f1 | rev)

            lastbarcode=$(echo $lastcall_p | rev | cut -d"/" -f1 | rev)

            if [[ $verbose == true ]]; then

                echo "current file: $currentbarcode"

                echo "last file: $lastbarcode"

            fi

            if [[ ${barcodelength} == ${lastcall_b} ]] && [[ ${umilength} == ${lastcall_u} ]] && [[ ${barcodefile} == ${lastcall_p} ]]; then

                echo " call accepted: no conflict detected with other jobs currently running"

                #add current job to lock

                if [[ $setup == "false" ]]; then 

                    echo $lock > $lockfile

                fi

            #compare filenames (not paths) if not custom barcodes

            elif [[ ${barcodelength} == ${lastcall_b} ]] && [[ ${umilength} == ${lastcall_u} ]] && [[ $currentbarcode == "AllPossibilities_"* ]] && [[ $lastbarcode == "AllPossibilities_"* ]]; then

                echo " call accepted: no conflict detected with other jobs currently running"

                #add current job to lock

                lock=$(($lock+1))

                if [[ $setup == "false" ]]; then 

                    echo $lock > $lockfile

                fi

            else

                echo "Error: conflict between technology selected for the new job and other jobs currently running"

                echo "make sure that the barcode length, UMI length, and the whitelist barcodes are the same as the other jobs currently running"