isoseq-pipeline/cluster.yaml at master · RajLabMSSM/isoseq-pipeline · GitHub

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# cluster.yaml
# set job submission parameters for each rule
# himem - default should be "", "-R himem" if you need the himem nodes
__default__:
  queue: express
  cores: 8
  mem: 3000
  time: '120'
  name: $(basename $(pwd)):{rule}:{wildcards}
  output: logs/{rule}:{wildcards}.stdout
  error: logs/{rule}:{wildcards}.stderr
  himem: ""
run_stringtie:
  cores: 4
  mem: 6000
  time: 720
merge_stringtie:
  cores: 8
  mem: 3000
  time: 720
talon_filter:
  cores: 1
  mem: 30000
  queue: premium
  time: 720
  himem: "-R himem"
talon_label_reads:
  cores: 8
  mem: 3000
  time: 500
cupcake_collapse:
    cores: 16
    mem: 24000
    time: '144:00'
    queue: premium
    himem: "-R himem"
run_bambu:
  cores: 8
  mem: 24000
  time: 72:00
  queue: premium
  himem: "-R himem"
run_isoquant:
  cores: 8
  mem: 24000
  time: 72:00
  queue: premium
  himem: "-R himem"
run_talon_simul:
  cores: 8
  mem: 24000
  time: 72:00
  queue: premium
  himem: "-R himem"
merge_flnc_bams:
  cores: 1
  mem: 3000
  time: 1440
  queue: premium
chain_samples:
    time: '180'
    mem: 3000
    cores: 30
samtools:
    cores: 8
    mem: 3000
    time: 60
minimap:
    cores: 16
    mem: 3000
    time: 360
nanopore_alignment:
    cores: 4
    mem: 24000
    time: 360
    himem: "-R himem"
SQANTI:
    time: 720
    mem: 3000
    cores: 8
TAMA_collapse:
    cores: 16
    mem: 3000
    time: 60
CCS:
   time: 72:00
   queue: 'long'
   mem: 25000
   cores: 36
LIMA:
   cores: 2
   mem: 12000
refine:
   cores: 4
   mem: 25000
align_flnc_bam:
   cores: 16
   mem: 3000
   time: 720
split_flnc_bam:
    cores: 1
    mem: 3000
    time: 719
split_unmapped_flnc_bam:
    cores: 1
    mem: 3000
    time: 719
isoseq3_cluster:
   queue: premium
   cores: 28
   mem: 3000
   time: 2880
   #himem: "-R himem"
demultiplex_abundances:
    cores: 16
    mem: 3000
    time: '720'
    #himem: "-R himem"
sam_to_bam:
    cores: 4
    mem: 3000
    time: 360
fastqc:
    cores: 8
    mem: 3000
    time: 360