@include "_basic_sc_rna_counter_stages.mro"

call SORT_BY_POS(
    inputs = [
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk00-u40122a10e8/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk01-u40122a10e8/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk02-u40122a10e8/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk03-u40122a10e8/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk04-u40122a10e8/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk05-u40122a10e8/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk06-u40122a10e8/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk07-u40122a10e8/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk08-u40122a10e8/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk09-u40122a10e8/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk10-u40122a10e8/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk11-u40122a10e9/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk12-u40122a10e9/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk13-u40122a10e9/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk14-u40122a10e9/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk15-u40122a10e9/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk16-u40122a10e9/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk17-u40122a10e9/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk18-u40122a10e9/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk19-u40122a10e9/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk20-u40122a10e9/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk21-u40122a10e9/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk22-u40122a10e9/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk23-u40122a10e9/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk24-u40122a10e9/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk25-u40122a10e9/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk26-u40122a10ea/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk27-u40122a10ea/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk28-u40122a10ea/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk29-u40122a10ea/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk30-u40122a10ea/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk31-u40122a10ea/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk32-u40122a10ea/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk33-u40122a10ea/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk34-u40122a10ea/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk35-u40122a10ea/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk36-u40122a10ea/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk37-u40122a10ea/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk38-u40122a10ea/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk39-u40122a10ea/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk40-u40122a10eb/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk41-u40122a10eb/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk42-u40122a10eb/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk43-u40122a10eb/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk44-u40122a10eb/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk45-u40122a10eb/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk46-u40122a10eb/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk47-u40122a10eb/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk48-u40122a10eb/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk49-u40122a10eb/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk50-u40122a10eb/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk51-u40122a10eb/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk52-u40122a10eb/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk53-u40122a10eb/files/alignments.bam"
    ],
    num_threads = 6,
    mem_gb = 2,
)