Merge branch 'master' into kai

fi

##########

#check if chemistry matches expected input

#allow "auto" only for 10x

if [[ "$technology" != "10x" ]]; then

    #use SC3Pv3 (umi length 12) 

    if [[ $umilength -ge 11 ]] && [[ "$chemistry" == "SC3Pv1" ]] && [[ "$chemistry" == "SC3Pv2" ]]; then

        echo "Using 10x version 3 chemistry to support longer UMIs"

        chemistry="SC3Pv3"

    else

    #use SC3Pv2 (umi length 10)

        echo "Using 10x version 2 chemistry to support UMIs"

        chemistry="SC3Pv2"

    fi

    if [[ "$chemistry" != "SC3Pv1" ]] && [[ "$chemistry" != "SC3Pv2" ]] && [[ "$chemistry" != "SC3Pv3" ]] && [[ "$chemistry" != "SC5P-PE" ]] && [[ "$chemistry" != "SC5P-R2" ]]; then

        echo "Error: option --chemistry must be SC3Pv3, SC3Pv2, SC5P-PE , or SC5P-R2"

       exit 1

    fi

fi

#####checking if jobmode matches expected input#####