@include "_basic_sc_rna_counter_stages.mro"

call ALIGN_READS(
    reads = [
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk00-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk01-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk02-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk03-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk04-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk05-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk06-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk07-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk08-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk09-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk10-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk11-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk12-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk13-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk14-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk15-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk16-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk17-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk18-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk19-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk20-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk21-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk22-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk23-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk24-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk25-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk26-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk27-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk28-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk29-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk30-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk31-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk32-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk33-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk34-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk35-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk36-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk37-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk38-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk39-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk40-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk41-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk42-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk43-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk44-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk45-udfa1937459/files/reads.fastq/1.fastq.lz4"
    ],
    read2s = [],
    read_groups = [
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_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",
        "Gene Expression"
    ],
    reference_path = "/ufrc/ewang/lancetdenes/refdata-cellranger-mm10-3.0.0",
    threads = 4,
    max_hits_per_read = -1,
)