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locus.cluster_config.yaml
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locus.cluster_config.yaml
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__default__:
threads: 16
h_vmem: 2G
extra: ''
tmpdir: "$TMP"
log: '{wildcards.sample}/logs'
jobname: '{wildcards.sample}'
pythonpath: /hpcdata/bcbb/shared/microbiome_share/software/python3.9.5-GCCcore-10.3.0
## pythonpath has biom and plotnine libs installed
genomad:
modules: genomad/1.5.2
abund_genomad:
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
abund_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
abund_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'
iphop_abund:
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'
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