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ONT_pilot_gitlab
Commits
9177187f
Commit
9177187f
authored
Apr 14, 2021
by
Valentina Galata
Browse files
configs: removed not required steps (issue
#127
)
parent
e47143ef
Changes
4
Hide whitespace changes
Inline
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config/gdb/config.yaml
View file @
9177187f
...
...
@@ -2,10 +2,14 @@
# STEPS
# Steps to be done
steps
:
[
"
preprocessing"
,
"
assembly"
,
"
mapping"
,
"
annotation"
,
"
analysis"
,
"
taxonomy"
]
steps_annotation
:
[
"
rgi"
,
"
plasflow"
,
"
minced"
,
"
barrnap"
,
"
kegg"
]
# prodigal is run in any case
steps_analysis
:
[
"
quast"
,
"
mash"
,
"
mashmap"
,
"
fastani"
,
"
mummer"
,
"
cdhit"
,
"
diamond"
,
"
mmseqs2"
,
"
cov"
]
steps_taxonomy
:
[
"
kraken2"
,
"
kaiju"
]
# steps: ["preprocessing", "assembly", "mapping", "annotation", "analysis", "taxonomy"]
# steps_annotation: ["rgi", "plasflow", "minced", "barrnap", "kegg"] # prodigal is run in any case
# steps_analysis: ["quast", "mash", "mashmap", "fastani", "mummer", "cdhit", "diamond", "mmseqs2", "cov"]
# steps_taxonomy: ["kraken2", "kaiju"]
steps
:
[
"
preprocessing"
,
"
assembly"
,
"
mapping"
,
"
annotation"
,
"
analysis"
]
steps_annotation
:
[
"
rgi"
,
"
barrnap"
]
# prodigal is run in any case
steps_analysis
:
[
"
quast"
,
"
mash"
,
"
diamond"
,
"
mmseqs2"
,
"
cov"
]
steps_taxonomy
:
[]
############################################################
# INPUT
...
...
config/nwc/config.yaml
View file @
9177187f
...
...
@@ -2,10 +2,14 @@
# STEPS
# Steps to be done
steps
:
[
"
preprocessing"
,
"
assembly"
,
"
mapping"
,
"
annotation"
,
"
analysis"
,
"
taxonomy"
]
steps_annotation
:
[
"
rgi"
,
"
plasflow"
,
"
minced"
,
"
barrnap"
,
"
kegg"
]
# prodigal is run in any case
steps_analysis
:
[
"
quast"
,
"
mash"
,
"
mashmap"
,
"
fastani"
,
"
mummer"
,
"
cdhit"
,
"
diamond"
,
"
mmseqs2"
,
"
cov"
]
steps_taxonomy
:
[
"
kraken2"
,
"
kaiju"
]
# steps: ["preprocessing", "assembly", "mapping", "annotation", "analysis", "taxonomy"]
# steps_annotation: ["rgi", "plasflow", "minced", "barrnap", "kegg"] # prodigal is run in any case
# steps_analysis: ["quast", "mash", "mashmap", "fastani", "mummer", "cdhit", "diamond", "mmseqs2", "cov"]
# steps_taxonomy: ["kraken2", "kaiju"]
steps
:
[
"
preprocessing"
,
"
assembly"
,
"
mapping"
,
"
annotation"
,
"
analysis"
]
steps_annotation
:
[
"
rgi"
,
"
barrnap"
]
# prodigal is run in any case
steps_analysis
:
[
"
quast"
,
"
mash"
,
"
diamond"
,
"
mmseqs2"
,
"
cov"
]
steps_taxonomy
:
[]
############################################################
# INPUT
...
...
config/rumen/config.yaml
View file @
9177187f
...
...
@@ -2,10 +2,14 @@
# STEPS
# Steps to be done
steps
:
[
"
preprocessing"
,
"
assembly"
,
"
mapping"
,
"
annotation"
,
"
analysis"
,
"
taxonomy"
]
steps_annotation
:
[
"
rgi"
,
"
plasflow"
,
"
minced"
,
"
barrnap"
]
# prodigal is run in any case; excluded: kegg
steps_analysis
:
[
"
quast"
,
"
mash"
,
"
mashmap"
,
"
fastani"
,
"
cdhit"
,
"
diamond"
,
"
mmseqs2"
,
"
cov"
]
# excluded: mummer
steps_taxonomy
:
[
"
kraken2"
,
"
kaiju"
]
# steps: ["preprocessing", "assembly", "mapping", "annotation", "analysis", "taxonomy"]
# steps_annotation: ["rgi", "plasflow", "minced", "barrnap"] # prodigal is run in any case; excluded: kegg
# steps_analysis: ["quast", "mash", "mashmap", "fastani", "cdhit", "diamond", "mmseqs2", "cov"] # excluded: mummer
# steps_taxonomy: ["kraken2", "kaiju"]
steps
:
[
"
preprocessing"
,
"
assembly"
,
"
mapping"
,
"
annotation"
,
"
analysis"
]
steps_annotation
:
[
"
rgi"
,
"
barrnap"
]
# prodigal is run in any case
steps_analysis
:
[
"
quast"
,
"
mash"
,
"
diamond"
,
"
mmseqs2"
,
"
cov"
]
steps_taxonomy
:
[]
############################################################
# INPUT
...
...
config/zymo/config.yaml
View file @
9177187f
...
...
@@ -2,10 +2,14 @@
# STEPS
# Steps to be done
steps
:
[
"
preprocessing"
,
"
assembly"
,
"
mapping"
,
"
annotation"
,
"
analysis"
,
"
taxonomy"
]
steps_annotation
:
[
"
rgi"
,
"
plasflow"
,
"
minced"
,
"
barrnap"
,
"
kegg"
]
# prodigal is run in any case
steps_analysis
:
[
"
quast"
,
"
mash"
,
"
mashmap"
,
"
fastani"
,
"
mummer"
,
"
cdhit"
,
"
diamond"
,
"
mmseqs2"
,
"
cov"
]
steps_taxonomy
:
[
"
kraken2"
,
"
kaiju"
]
# steps: ["preprocessing", "assembly", "mapping", "annotation", "analysis", "taxonomy"]
# steps_annotation: ["rgi", "plasflow", "minced", "barrnap", "kegg"] # prodigal is run in any case
# steps_analysis: ["quast", "mash", "mashmap", "fastani", "mummer", "cdhit", "diamond", "mmseqs2", "cov"]
# steps_taxonomy: ["kraken2", "kaiju"]
steps
:
[
"
preprocessing"
,
"
assembly"
,
"
mapping"
,
"
annotation"
,
"
analysis"
]
steps_annotation
:
[
"
rgi"
,
"
barrnap"
]
# prodigal is run in any case
steps_analysis
:
[
"
quast"
,
"
mash"
,
"
diamond"
,
"
mmseqs2"
,
"
cov"
]
steps_taxonomy
:
[]
############################################################
# INPUT
...
...
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