comment sources for inDrops

test/cellranger_reference/cellranger-tiny-ref/1.2.0/ filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/1.2.0/fasta filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/1.2.0/genes filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/1.2.0/pickle filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/1.2.0/reference.json filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/1.2.0/star filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0 filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/fasta filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/genes filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/pickle filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/reference.json filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/exonGeTrInfo.tab filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/genomeParameters.txt filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/sjdbList.fromGTF.out.tab filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/fasta/genome.fa filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/fasta/genome.fa.fai filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/pickle/genes.pickle filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/chrNameLength.txt filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/Genome filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/chrLength.txt filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/exonInfo.tab filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/geneInfo.tab filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/sjdbInfo.txt filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/sjdbList.out.tab filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/transcriptInfo.tab filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/genes/genes.gtf filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SAindex filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/chrName.txt filter=lfs diff=lfs merge=lfs -text

test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/chrStart.txt filter=lfs diff=lfs merge=lfs -text

        done

    fi

    #remove adapter from inDrops

    #remove adapter from inDrops see here for details:

     ## https://github.com/BUStools/bustools/issues/4

     ## https://teichlab.github.io/scg_lib_structs/methods_html/inDrop.html

    if [[ "$technology" == "indrop-v1" ]] || [[ "$technology" == "indrop-v2" ]]; then

        for convFile in "${convFiles[@]}"; do

            #remove adapter if present