Commit c2563441 authored by Valentina Galata's avatar Valentina Galata
Browse files

added workflow parameter to config.yaml and updated Snakefile (issue #24)

parent e0939b4e
#Snakefile
w = 'complete'
if w is 'complete':
if config["workflow"] == "complete":
include:
"workflows/Combine_PathoFact_workflow"
rule all:
......@@ -15,7 +13,7 @@ if w is 'complete':
],
OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]
)
elif w is 'Tox':
elif config["workflow"] == "Tox":
include:
"workflows/Toxin_workflow"
rule all:
......@@ -27,7 +25,7 @@ elif w is 'Tox':
],
OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]
)
elif w is 'Vir':
elif config["workflow"] == "Vir":
include:
"workflows/Virulence_workflow"
rule all:
......@@ -36,7 +34,7 @@ elif w is 'Vir':
"{OUTDIR}/{project}/Virulence_prediction_{input_file}_report.csv",
OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]
)
elif w is 'AMR':
elif config["workflow"] == "AMR":
include:
"workflows/AMR_workflow"
rule all:
......@@ -49,4 +47,4 @@ elif w is 'AMR':
OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]
)
else:
raise Exception('NO workflow selected')
raise Exception("Unknown workflow option: %s" % config["workflow"])
......@@ -12,6 +12,13 @@ OUTDIR: /path/to/samples
# Define size of split fasta files (default 10 000 sequences/file)
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 #
###########
......
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