iRODSdownloader_CellRangerRunGEX5prime.sh

#!/bin/bash
set -e
CPU=30
CELLRANGER=/home/ubuntu/tools/cellranger-3.0.2/cellranger
REFSEQ=/home/ubuntu/refseq/refdata-cellranger-GRCh38-3.0.0

for SAMPLE in 5891STDY80386{66..67}
    do
        echo "Processing: "$SAMPLE
        printf '#!/bin/bash\nset -e\n\n----\n' > imeta$SAMPLE.sh
        imeta qu -z seq -d sample = $SAMPLE and type = cram and target = 1 and library_type = 'Chromium single cell 5 prime' >> imeta$SAMPLE.sh
        sed ':a;N;$!ba;s/----\ncollection:/iget -K/g' -i imeta$SAMPLE.sh
        sed ':a;N;$!ba;s/\ndataObj: /\//g' -i imeta$SAMPLE.sh
        bash imeta$SAMPLE.sh
        parallel bash ~/tools/linuxshell-genomics/cramfastq.sh ::: *.cram
        rm -f *.cram
        count=1
        for file in *I1_001.fastq.gz
            do
                mv "${file}" "${file/*.cram/$SAMPLE\_S$count\_L001}"
                file=$(sed 's/I1/R1/g' <<< $file)
                mv "${file}" "${file/*.cram/$SAMPLE\_S$count\_L001}"
                file=$(sed 's/R1/R2/g' <<< $file)
                mv "${file}" "${file/*.cram/$SAMPLE\_S$count\_L001}"
                (( count++ ))
            done
        mkdir -p fastq-$SAMPLE && mv *.fastq.gz fastq-$SAMPLE

        $CELLRANGER count --localcores $CPU --id=$SAMPLE --transcriptome=$REFSEQ \
        --fastqs=fastq-$SAMPLE \
        --sample=$SAMPLE
        rm -r ./$SAMPLE/SC_* ./$SAMPLE/*.tgz ./$SAMPLE/_* ./fastq-$SAMPLE
done