update dropseq tests for check file names

fi

# test manual setup

bash launch_universc.sh -t "nadia" --setup

# remove processed files

if [[ -f SRR1873277_S1_L001_R[12]_001.fastq ]]; then

    rm SRR1873277_S1_L001_R[12]_001.fastq

fi

# call on dropseq with files

bash launch_universc.sh --id "test-dropseq" --technology "nadia" \

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

 --read1 "test/shared/dropseq-test/SRR1873277_S1_L001_R1_001" \

 --read2 "test/shared/dropseq-test/SRR1873277_S1_L001_R2_001" 

 --read1 "test/shared/dropseq-test/SRR1873277_Sample1_R1" \

 --read2 "test/shared/dropseq-test/SRR1873277_Sample1_R2" 

#reset test data (files names)

if [[ -f test/shared/dropseq-test/SRR1873277_S1_L001_R[12]_001.fastq ]];

    gzip test/shared/dropseq-test/SRR1873277_S1_L001_R[12]_001.fastq

fi

if [[ ! -f test/shared/dropseq-test/SRR1873277_Sample1_R1.fastq.gz ]]; then

    mv test/shared/dropseq-test/SRR1873277_S1_L001_R1_001.fastq.gz test/shared/dropseq-test/SRR1873277_Sample1_R1.fastq.gz

else

    rm test/shared/dropseq-test/SRR1873277_S1_L001_R1_001.fastq.gz

fi

if [[ ! -f test/shared/dropseq-test/SRR1873277_Sample1_R2.fastq.gz ]]; then

    mv test/shared/dropseq-test/SRR1873277_S1_L001_R2_001.fastq.gz test/shared/dropseq-test/SRR1873277_Sample1_R1.fastq.gz

else

    rm test/shared/dropseq-test/SRR1873277_S1_L001_R2_001.fastq.gz

fi

# compress all input files

if [[ -f test/shared/dropseq-test/*fastq ]]; then

    gzip -f test/shared/dropseq-test/*fastq

    gzip test/shared/dropseq-test/*fastq

fi