@include "_basic_sc_rna_counter_stages.mro"

call ALIGN_READS(
    reads = [
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk00-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk01-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk02-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk03-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk04-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk05-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk06-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk07-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk08-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk09-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk10-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk11-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk12-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk13-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk14-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk15-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk16-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk17-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk18-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk19-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk20-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk21-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk22-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk23-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk24-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk25-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk26-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk27-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk28-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk29-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk30-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk31-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk32-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk33-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk34-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk35-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk36-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk37-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk38-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk39-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk40-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk41-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk42-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk43-u85e8937216/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk44-u85e8937216/files/reads.fastq/1.fastq.lz4"
    ],
    read2s = [],
    read_groups = [
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1",
        "h2b_run2:0:1:HJ5NCBGXB:1"
    ],
    library_types = [
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression"
    ],
    reference_path = "/ufrc/ewang/lancetdenes/refdata-cellranger-mm10-3.0.0",
    threads = 4,
    max_hits_per_read = -1,
)