cluster.yaml

__default__:
  jobname: "{rule}.{wildcards}"
  nodes: 1
  ntaskspernode: 1
  cpuspertask: 1
  mempercpu: "4GB"
  time: "30:00"
  account: "ACCOUNT"
  partition: "standard"
  mailuser: "EMAIL"
  mailtype: "END,FAIL"
  output: "logs/slurm/%x-%j.out"





# Part 1: Read Processing ---------------------------------

trimReadPair:
  cpuspertask: 2
  time: "45:00"

buildContaminantIndices:
  cpuspertask: 12
  time: "4:00:00"

decontaminateTrimmedReads:
  cpuspertask: 4
  time: "5:00:00"

# Part 2: Assembly ----------------------------------------

assembleReads:
  cpuspertask: 16
  time: "8:00:00"

dedupeContigs:
  cpuspertask: 12

# Part 3: Viral Contig Curation ---------------------------

predictContigsVirsorter:
  cpuspertask: 12
  time: "36:00:00"

predictContigsVirfinder:
  cpuspertask: 12
  time: "3:00:00"

# Part 4: Binning -----------------------------------------

indexContigs:
  cpuspertask: 12

mapContigs:
  cpuspertask: 6
  time: "2:00:00"

binContigs:
  cpuspertask: 16
  time: "2:00:00"

detectBinContamination:
  cpuspertask: 12
  time: "6:00:00"

# Part 5: Generate Shared Bin File ------------------------

indexBins:
  cpuspertask: 12
  time: "2:00:00"

mapBins:
  cpuspertask: 6
  time: "2:00:00"

# Part 6: Taxonomic Classification ------------------------

getClassificationDatabases:
  cpuspertask: 4
  mempercpu: "45GB"
  time: "1:30:00"

classifyBins:
  cpuspertask: 12
  time: "1:30:00"

# # Part 7: Diversity Metrics -------------------------------

calcBinAlphaDiversity:
  cpuspertask: 24
  mempercpu: "2GB"
  time: "12:00:00"

calcBinBetaDiversity:
  cpuspertask: 24
  mempercpu: "2GB"
  time: "12:00:00"

# Part 8: Quality Control ---------------------------------

combineRawReports:
  cpuspertask: 12

combineTrimmedReports:
  cpuspertask: 12

combineDeconReports:
  cpuspertask: 12

assemblyStats:
  cpuspertask: 4