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Laura Denies
PathoFact
Commits
c2563441
Commit
c2563441
authored
Apr 21, 2020
by
Valentina Galata
Browse files
added workflow parameter to config.yaml and updated Snakefile (issue
#24
)
parent
e0939b4e
Changes
2
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Snakefile
View file @
c2563441
#Snakefile
#Snakefile
w = 'complete'
if config["workflow"] == "complete":
if w is 'complete':
include:
include:
"workflows/Combine_PathoFact_workflow"
"workflows/Combine_PathoFact_workflow"
rule all:
rule all:
...
@@ -15,7 +13,7 @@ if w is 'complete':
...
@@ -15,7 +13,7 @@ if w is 'complete':
],
],
OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]
OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]
)
)
elif
w is '
Tox
'
:
elif
config["workflow"] == "
Tox
"
:
include:
include:
"workflows/Toxin_workflow"
"workflows/Toxin_workflow"
rule all:
rule all:
...
@@ -27,7 +25,7 @@ elif w is 'Tox':
...
@@ -27,7 +25,7 @@ elif w is 'Tox':
],
],
OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]
OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]
)
)
elif
w is '
Vir
'
:
elif
config["workflow"] == "
Vir
"
:
include:
include:
"workflows/Virulence_workflow"
"workflows/Virulence_workflow"
rule all:
rule all:
...
@@ -36,7 +34,7 @@ elif w is 'Vir':
...
@@ -36,7 +34,7 @@ elif w is 'Vir':
"{OUTDIR}/{project}/Virulence_prediction_{input_file}_report.csv",
"{OUTDIR}/{project}/Virulence_prediction_{input_file}_report.csv",
OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]
OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]
)
)
elif
w is '
AMR
'
:
elif
config["workflow"] == "
AMR
"
:
include:
include:
"workflows/AMR_workflow"
"workflows/AMR_workflow"
rule all:
rule all:
...
@@ -49,4 +47,4 @@ elif w is 'AMR':
...
@@ -49,4 +47,4 @@ elif w is 'AMR':
OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]
OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]
)
)
else:
else:
raise Exception(
'NO
workflow
selected'
)
raise Exception(
"Unknown
workflow
option: %s" % config["workflow"]
)
config.yaml
View file @
c2563441
...
@@ -12,6 +12,13 @@ OUTDIR: /path/to/samples
...
@@ -12,6 +12,13 @@ OUTDIR: /path/to/samples
# Define size of split fasta files (default 10 000 sequences/file)
# Define size of split fasta files (default 10 000 sequences/file)
size_fasta
:
100000
size_fasta
:
100000
# Workflow (default: "complete")
# complete: complete pipeline: toxin + virulence + (AMR + MGE) prediction
# Tox: toxin prediction
# Vir: virulence prediction
# AMR: antimicrobial resistance (AMR) & mobile genetic element (MGE) prediction
workflow
:
"
complete"
###########
###########
# SignalP #
# SignalP #
###########
###########
...
...
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