Commit ff3918e0 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

add inputs for new technologies: bd-rhapsody, microwell-seq, split-seq, strt-seq

parent 754f3e9f

launch_universc.sh

+51 −1
Original line number Diff line number Diff line
@@ -603,6 +603,8 @@ elif [[ "$technology" == "celseq" ]] || [[ "$technology" == "cel-seq" ]]; then 
    technology="celseq"

elif [[ "$technology" == "celseq2" ]] || [[ "$technology" == "cel-seq2" ]]; then

    technology="celseq2"

elif [[ "$technology" == "bd-rhapsody" ]] || [[ "$technology" == "bd" ]] || [[ "$technology" == "rhapsody" ]] || [[ "$technology" == "bdrhapsody" ]]; then

    technology="bd-rhapsody"

elif [[ "$technology" == "nadia" ]] || [[ "$technology" == "dropseq" ]] || [[ "$technology" == "drop-seq" ]]; then

    technology="nadia"

elif [[ "$technology" == "icell8" ]] || [[ "$technology" == "icell-8" ]]; then
@@ -617,6 +619,8 @@ elif [[ "$technology" == "marsseq" ]] || [[ "$technology" == "mars-seq" ]] || [[ 
    technology="marsseq-v1"

elif [[ "$technology" == "marsseq2" ]] || [[ "$technology" == "mars-seq2" ]] || [[ "$technology" == "marsseq-v2" ]] || [[ "$technology" == "mars-seq-v2" ]] || [[ "$technology" == "marsseqv2" ]] || [[ "$technology" == "mars-seqv2" ]]; then

    technology="marsseq-v2"

elif [[ "$technology" == "microwell-seq" ]] || [[ "$technology" == "micro-well" ]] || [[ "$technology" == "microwell" ]] || [[ "$technology" == "microwellseq" ]]; then

     technology="microwellseq"

elif [[ "$technology" == "quartz-seq2-384" ]] || [[ "$technology" == "quartzseq2-384" ]] || [[ "$technology" == "quartz-seq2-v3.1" ]] || [[ "$technology" == "quartzseq2-v3.1" ]] || [[ "$technology" == "quartzseq2v3.1" ]]; then

    technology="quartz-seq2-384"

elif [[ "$technology" == "quartz-seq2-1536" ]] || [[ "$technology" == "quartzseq2-1536" ]] || [[ "$technology" == "quartz-seq2-v3.2" ]] || [[ "$technology" == "quartzseq2-v3.2" ]] || [[ "$technology" == "quartzseq2v3.2" ]]; then
@@ -644,6 +648,12 @@ elif [[ "$technology" == "splitseq" ]] || [[ "$technology" == "split-seq" ]]; th 
    technology="splitseq"

elif [[ "$technology" == "splitseq2" ]] || [[ "$technology" == "split-seq2" ]] || [[ "$technology" == "splitseq-v2" ]] || [[ "$technology" == "split-seq-v2" ]]; then

    technology="splitseq2"

elif [[ "$technology" == "strt-seq" ]] || [[ "$technology" == "strt" ]] || [[ "$technology" == "strtseq" ]]; then

     technology="strt-seq"

elif [[ "$technology" == "strt-seq-c1" ]] || [[ "$technology" == "strt-seqc1" ]] || [[ "$technology" == "strtseqc1" ]] || [[ "$technology" == "strtseq-c1" ]]; then

     technology="strt-seq-c1"

elif [[ "$technology" == "strt-seq-2i" ]] || [[ "$technology" == "strt-seq2i" ]] || [[ "$technology" == "strtseq2i" ]] || [[ "$technology" == "strtseq-2i" ]]; then

     technology="strt-seq-2i"

elif [[ "$technology" == "surecell" ]] || [[ "$technology" == "surecellseq" ]] || [[ "$technology" == "surecell-seq" ]] || [[ "$technology" == "ddseq" ]] || [[ "$technology" == "dd-seq" ]] || [[ "$technology" == "bioraad" ]]; then

    technology="surecell"

elif [[ "$technology" == "custom"* ]]; then
@@ -707,6 +717,10 @@ elif [[ "$technology" == "10x-v3" ]]; then 
    barcodelength=16

    umilength=12

    minlength=16

elif [[ "$technology" == "bd-rhapsody" ]]; then

    barcodelength=27

    umilength=8

    minlength=27

elif [[ "$technology" == "celseq" ]]; then

    barcodelength=8

    umilength=4
@@ -735,6 +749,10 @@ elif [[ "$technology" == "marsseq-v1" ]]; then 
    barcodelength=6

    umilength=10

    minlength=6

elif [[ "$technology" == "microwellseq" ]]; then

    barcodelength=18

    umilength=6

    minlength=18

elif [[ "$technology" == "marsseq-v2" ]]; then

    barcodelength=7

    umilength=8
@@ -779,6 +797,18 @@ elif [[ "$technology" == "splitseq2" ]]; then 
     barcodelength=24

     umilength=10

     minlength=24

elif [[ "$technology" == "strt-seq" ]]; then

    barcodelength=6

    umilength=0

    minlength=6

elif [[ "$technology" == "strt-seq-c1" ]]; then

    barcodelength=8

    umilength=5

    minlength=8

elif [[ "$technology" == "strt-seq-2i" ]]; then

    barcodelength=13

    umilength=6

    minlength=13

elif [[ "$technology" == "surecell" ]]; then

    barcodelength=18

    umilength=8
@@ -1494,7 +1524,7 @@ if [[ -n "$barcodefile" ]]; then 
        #getting absolute path

        barcodefile=$(readlink -f $barcodefile)

        #allowing WellList from ICELL8 and other well-based techniques

        if [[ "$technology" == "icell8" ]] || [[ "$technology" == "quartz-seq2*" ]] || [[ "$technology" == "splitseq" ]]|| [[ "$technology" == "splitseq2" ]] || [[ "$technology" == "smartseq*" ]] || [[ "$technology" == "seqwell" ]] || [[ "$technology" == "sciseq2" ]] || [[ "$technology" == "sciseq3" ]] || [[ "$technology" == "custom" ]]; then

        if [[ "$technology" == "bd-rhapsody" ]] || [[ "$technology" == "icell8" ]] || [[ "$technology" == "quartz-seq2*" ]] || [[ "$technology" == "microwellseq" ]] || [[ "$technology" == "smartseq*" ]] || [[ "$technology" == "seqwell" ]] || [[ "$technology" == "sciseq2" ]] || [[ "$technology" == "sciseq3" ]] || [[ "$technology" == "splitseq" ]] || [[ "$technology" == "splitseq2" ]] || [[ "$technology" == "custom" ]]; then

            seg=$'\t'

            n_col=$(awk -F'\t' '{print NF}' $barcodefile | sort -nu | tail -n 1)

            if [[ $n_col -eq 1 ]]; then
@@ -1528,11 +1558,21 @@ if [[ -n "$barcodefile" ]]; then 
else

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

        barcodefile="default:10x"

    elif [[ "$technology" == "bd-rhapsody" ]]; then

             barcodefile=${whitelistdir}/bd_rhapsody_barcode.txt

             if [[ ! -f ${whitelistdir}/bd_rhapsody_barcode.txt ]]; then

                 echo "  ...generating combination of I1, I2, and RT barcodes..."

             fi

    elif [[ "$technology" == "icell8" ]]; then

        barcodefile=${whitelistdir}/ICELL8_barcode.txt

	echo "***WARNING: selected barcode file (${barcodefile}) contains barcodes for all wells in ICELL8. valid barcode will be an overestimate***"

    elif [[ "$technology" == "marsseq-v2" ]]; then

        barcodefile=${whitelistdir}/MARS-Seq2_barcode.txt

    elif [[ "$technology" == "microwellseq" ]]; then

             barcodefile=${whitelistdir}/microwellseq_barcode.txt

             if [[ ! -f ${whitelistdir}/microwellseq_barcode.txt ]]; then

                 echo "  ...generating combination of I1, I2, and RT barcodes..."

             fi

    elif [[ "$technology" == "quartz-seq2-384" ]]; then

        barcodefile=${whitelistdir}/Quartz-Seq2-384_barcode.txt

    elif [[ "$technology" == "quartz-seq2-1536" ]]; then
@@ -1559,6 +1599,16 @@ else 
             if [[ ! -f ${whitelistdir}/sciseq3_barcode.txt ]]; then

                 echo "  ...generating combination of I1, I2, and RT barcodes..."

             fi

    elif [[ "$technology" == "splitseq" ]]; then

             barcodefile=${whitelistdir}/splitseq_barcode.txt

             if [[ ! -f ${whitelistdir}/splitseq_barcode.txt ]]; then

                 echo "  ...generating combination of I1, I2, and RT barcodes..."

             fi

    elif [[ "$technology" == "splitseq2" ]]; then

             barcodefile=${whitelistdir}/splitseq2_barcode.txt

             if [[ ! -f ${whitelistdir}/splitseq2_barcode.txt ]]; then

                 echo "  ...generating combination of I1, I2, and RT barcodes..."

             fi

    elif [[ "$technology" == "smartseq3" ]]; then

        barcodefile=${whitelistdir}/SmartSeq3_barcode.txt

    else

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