locus.cluster_config.yaml

__default__:
    threads: 16
    h_vmem: 2G
    extra: ''
    tmpdir: "$TMP"
    log: '{wildcards.sample}/logs'
    jobname: '{wildcards.sample}'


genomad:
  modules: genomad/1.5.2

verse:
  threads: 8
  modules:
    - verse/0.1.5
    - Python/3.9.5-GCCcore-10.3.0

checkv:
  threads: 8
  h_vmem: 2G
  modules:
    - checkv/0.8.1
    - Python/2.7.15-foss-2018b

checkv_filter:
  threads: 2
  h_vmem: 8G
  extra: '-l quick'
  modules: seqtk/1.3-r106


bbtools_dedupe:
  threads: 8
  h_vmem: 8G
  modules: bbmap/38.90
  log: 'logs'
  jobname: 'all'

mmseqs:
  h_vmem: 15G
  extra: '-l himem'
  modules:
    - mmseqs2/14.7e284
    - Python/3.9.5-GCCcore-10.3.0
  log: 'logs'
  jobname: 'all'

votu:
  threads: 2
  h_vmem: 4G
  extra: '-l quick'
  modules:
    - Python/3.9.5-GCCcore-10.3.0
    - krona/2.7.1
  log: 'logs'
  jobname: 'all'

vs4dramv:
  modules: virsorter/2.2.3-Python-3.8.10

dramv:
  h_vmem: 3G
  modules: /hpcdata/bcbb/shared/microbiome_share/modules/dram/1.4.6_ms

verse_dramv:
  threads: 8
  h_vmem: 8G
  modules:
    - verse/0.1.5
    - Python/3.9.5-GCCcore-10.3.0
    - liftoff/1.6.3-Python-3.9.12

gene_tables:
  threads: 2
  h_vmem: 4G
  extra: '-l quick'
  modules: Python/3.9.5-GCCcore-10.3.0
  log: 'logs'
  jobname: 'all'

amgs:
  h_vmem: 3G
  modules: /hpcdata/bcbb/shared/microbiome_share/modules/dram/1.4.6_ms

# not sure why we needs this twice, but Locus didn't like re-using the
# verse_dramv rule
verse_amgs:
  threads: 8
  h_vmem: 8G
  extra: '-l quick'
  modules:
    - verse/0.1.5
    - Python/3.9.5-GCCcore-10.3.0
    - liftoff/1.6.3-Python-3.9.12

amg_tables:
  threads: 2
  h_vmem: 4G
  extra: '-l quick'
  modules: Python/3.9.5-GCCcore-10.3.0
  log: 'logs'
  jobname: 'all'


    
iphop:
  h_vmem: 15G
  extra: '-l himem'
  modules:
    - iphop/1.3.0
  log: 'logs'
  jobname: 'all'

diamond:
  threads: 8
  h_vmem: 12G
  modules: diamond/2.0.15.153
  tmpdir: /tmp
  ## on Locus /tmp is on local disk but $TMP is not and for diamond this matters