/
bacteria.yaml
73 lines (73 loc) · 1.92 KB
/
bacteria.yaml
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general:
protein_xref: '~/database/protein.sqlite'
CDS:
prodigal:
params: '-f gff'
priority: 100
threads: 1
rho_independent_terminator:
transtermhp:
params: '-p $TRANSTERMHP'
# '--all-context' # output all predicted terminators instead of legitimate ones
priority: 99
threads: 1
ncRNA:
cmscan:
params: ''
priority: 50
threads: 1
db: '~/database/Rfam/v12.2/rfam-tRNA-rRNA.cm'
output: 'cmscan'
CRISPR:
minced:
params: ''
priority: 50
threads: 1
tRNA:
aragorn:
params: '-w'
priority: 50
threads: 1
tandem_repeats:
tandem_repeats_finder:
params: ''
priority: 50
threads: 1
output: 'tandem_repeats_finder'
rRNA:
rnammer:
params: '-m lsu,ssu,tsu'
# cmscan_rRNA:
# params: ''
# priority: 50
# threads: 1
# db: '/Users/zech/database/Rfam/v12.2/bacteria.cm'
protein:
diamond_uniref90:
params: '--index-chunks 1 --id 90 --subject-cover 80 --query-cover 80 --max-target-seqs 3'
priority: 50
threads: 1
db: '~/database/uniref/20161130/uniref90.dmnd'
input: 'prodigal.faa'
output: 'diamond_uniref90.faa'
diamond_uniref50:
params: '--index-chunks 1 --id 50 --subject-cover 80 --query-cover 80 --max-target-seqs 3'
priority: 50
threads: 1
db: '~/database/uniref/20161130/uniref50.dmnd'
input: 'diamond_uniref90.faa'
output: 'diamond_uniref50.faa'
# hmmscan_tigrfam:
# params: '−−cug_nc'
# priority: 60
# threads: 1
# db: '~/database/TIGRFAM/tigrfam.hmm'
# input: ''
# output: ''
# hmmscan_tigrfam:
# params: '−−cug_ga'
# priority: 60
# threads: 1
# db: '~/database/TIGRFAM/tigrfam.hmm'
# input: ''
# output: ''