test smart-seq3 with custom barcode whitelists

    rm -rf test-smartseq3

fi

whitelistdir=whitelists

join -j 9999 ${whitelistdir}/Aligent_SureSelectXT_Index1_i7_barcodes.txt  ${whitelistdir}/Aligent_SureSelectXT_Index2_i5_barcodes.txt | sed "s/ //g" > ${whitelistdir}/Aligent_SureSelectXT_dual_barcodes.txt

if [[ ! -f SmartSeq3_test_barcodes.txt ]]; then

    gunzip -k SmartSeq3_test_barcodes.txt.gz

fi

# call on smartseq3 with files

bash launch_universc.sh --id "test-smartseq3" --technology "smartseq" \

 --reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \

 --read1 "test/shared/smartseq3-test/Smartseq3_diySpike_R1" \

 --read2 "test/shared/smartseq3-test/Smartseq3_diySpike_R2" \

 --barcodefile "${whitelistdir}/Aligent_SureSelectXT_dual_barcodes.txt" \

 --barcodefile "${whitelistdir}/SmartSeq3_test_barcodes.txt" \

 --jobmode "local" --localcores 1