@include "_basic_sc_rna_counter_stages.mro"

call ALIGN_READS(
    reads = [
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk00-u99f6b311cb/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk01-u99f6b311cb/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk02-u99f6b311cb/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk03-u99f6b311cb/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk04-u99f6b311cb/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk05-u99f6b311cc/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk06-u99f6b311cc/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk07-u99f6b311cc/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk08-u99f6b311cc/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk09-u99f6b311cc/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk10-u99f6b311cc/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk11-u99f6b311cc/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk12-u99f6b311cc/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk13-u99f6b311cc/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk14-u99f6b311cc/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk15-u99f6b311cc/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk16-u99f6b311cc/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk17-u99f6b311cc/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk18-u99f6b311cc/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk19-u99f6b311cc/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk20-u99f6b311cd/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk21-u99f6b311cd/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk22-u99f6b311cd/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk23-u99f6b311cd/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk24-u99f6b311cd/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk25-u99f6b311cd/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk26-u99f6b311cd/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk27-u99f6b311cd/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk28-u99f6b311cd/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk29-u99f6b311cd/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk30-u99f6b311cd/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk31-u99f6b311cd/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk32-u99f6b311cd/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk33-u99f6b311cd/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk34-u99f6b311cd/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk35-u99f6b311ce/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk36-u99f6b311ce/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk37-u99f6b311ce/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk38-u99f6b311ce/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk39-u99f6b311ce/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk40-u99f6b311ce/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk41-u99f6b311ce/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk42-u99f6b311ce/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk43-u99f6b311ce/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk44-u99f6b311ce/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk45-u99f6b311ce/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk46-u99f6b311ce/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk47-u99f6b311ce/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk48-u99f6b311ce/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk49-u99f6b311ce/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk50-u99f6b311ce/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk51-u99f6b311cf/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk52-u99f6b311cf/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk53-u99f6b311cf/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk54-u99f6b311cf/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk55-u99f6b311cf/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk56-u99f6b311cf/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk57-u99f6b311cf/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk58-u99f6b311cf/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk59-u99f6b311cf/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk60-u99f6b311cf/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk61-u99f6b311cf/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk62-u99f6b311d0/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk63-u99f6b311d0/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk64-u99f6b311d0/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk65-u99f6b311d0/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk66-u99f6b311d0/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk67-u99f6b311d0/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk68-u99f6b311d0/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk69-u99f6b311d0/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk70-u99f6b311d0/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk71-u99f6b311d0/files/reads.fastq/1.fastq.lz4"
    ],
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    ],
    library_types = [
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        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
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        "Gene Expression",
        "Gene Expression",
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        "Gene Expression",
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        "Gene Expression",
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        "Gene Expression",
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        "Gene Expression",
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        "Gene Expression",
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        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression"
    ],
    reference_path = "/restricted/projectnb/waxmanlab/kkarri/tabula_muris/drop-seq/mm10_ref/updated-usethis-mm10plus-pcg-ercc-lnc-nodups",
    threads = 4,
    max_hits_per_read = -1,
)