@include "_basic_sc_rna_counter_stages.mro"

call SORT_BY_POS(
    inputs = [
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk00-u48a5c0ca73/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk01-u48a5c0ca73/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk02-u48a5c0ca73/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk03-u48a5c0ca73/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk04-u48a5c0ca73/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk05-u48a5c0ca73/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk06-u48a5c0ca73/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk07-u48a5c0ca74/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk08-u48a5c0ca74/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk09-u48a5c0ca74/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk10-u48a5c0ca74/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk11-u48a5c0ca74/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk12-u48a5c0ca74/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk13-u48a5c0ca74/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk14-u48a5c0ca74/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk15-u48a5c0ca74/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk16-u48a5c0ca74/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk17-u48a5c0ca74/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk18-u48a5c0ca74/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk19-u48a5c0ca74/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk20-u48a5c0ca74/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk21-u48a5c0ca74/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk22-u48a5c0ca75/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk23-u48a5c0ca75/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk24-u48a5c0ca75/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk25-u48a5c0ca75/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk26-u48a5c0ca75/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk27-u48a5c0ca75/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk28-u48a5c0ca75/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk29-u48a5c0ca75/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk30-u48a5c0ca75/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk31-u48a5c0ca75/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk32-u48a5c0ca75/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk33-u48a5c0ca75/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk34-u48a5c0ca75/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk35-u48a5c0ca75/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk36-u48a5c0ca75/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk37-u48a5c0ca76/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk38-u48a5c0ca76/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk39-u48a5c0ca76/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk40-u48a5c0ca76/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk41-u48a5c0ca76/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk42-u48a5c0ca76/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk43-u48a5c0ca76/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk44-u48a5c0ca76/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk45-u48a5c0ca76/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk46-u48a5c0ca76/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk47-u48a5c0ca76/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk48-u48a5c0ca76/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk49-u48a5c0ca76/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk50-u48a5c0ca76/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk51-u48a5c0ca76/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk52-u48a5c0ca77/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk53-u48a5c0ca77/files/alignments.bam"
    ],
    num_threads = 6,
    mem_gb = 2,
)