Commit 1ac4fe80 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

detect custom barcode input as variable

parent 6d051a09
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+2 −0
Original line number Diff line number Diff line
@@ -1458,6 +1458,7 @@ if [[ $verbose ]]; then
    echo " setting whitelist barcode file."
fi

custombarcodes=false
if [[ -n "$barcodefile" ]]; then
    if [[ ! -f $barcodefile ]]; then
        echo "Error: File selected for option --barcodefile does not exist"
@@ -1465,6 +1466,7 @@ if [[ -n "$barcodefile" ]]; then
    else
        #getting absolute path
        barcodefile=$(readlink -f $barcodefile)
        custombarcodes=true
        #allowing WellList from ICELL8 and other well-based techniques
        if [[ "$technology" == "icell8" ]] || [[ "$technology" == "quartz-seq2*" ]] || [[ "$technology" == "splitseq" ]] || [[ "$technology" == "smartseq*" ]] || [[ "$technology" == "seqwell" ]] || [[ "$technology" == "sciseq" ]] || [[ "$technology" == "custom" ]]; then
            seg=$'\t'