Commit 086684df authored by Valentina Galata's avatar Valentina Galata
Browse files

format fix in Snakefile (issue #26)

parent 616d46cd
...@@ -3,40 +3,50 @@ ...@@ -3,40 +3,50 @@
w = 'complete' w = 'complete'
if w is 'complete': if w is 'complete':
include: include:
"workflows/Combine_PathoFact_workflow" "workflows/Combine_PathoFact_workflow"
rule all: rule all:
input: input:
expand(["{OUTDIR}/{project}/AMR/{input_file}_AMR_MGE_prediction_detailed.tsv", expand(
"{OUTDIR}/{project}/Toxin_gene_library_{input_file}_report.tsv", [
"{OUTDIR}/{project}/PathoFact_{input_file}_predictions.csv"], "{OUTDIR}/{project}/AMR/{input_file}_AMR_MGE_prediction_detailed.tsv",
OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]) "{OUTDIR}/{project}/Toxin_gene_library_{input_file}_report.tsv",
"{OUTDIR}/{project}/PathoFact_{input_file}_predictions.csv"
],
OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]
)
elif w is 'Tox': elif w is 'Tox':
include: include:
"workflows/Toxin_workflow" "workflows/Toxin_workflow"
rule all: rule all:
input: input:
expand(["{OUTDIR}/{project}/Toxin_prediction_{input_file}_report.csv", expand(
"{OUTDIR}/{project}/Toxin_gene_library_{input_file}_report.tsv"], [
OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]) "{OUTDIR}/{project}/Toxin_prediction_{input_file}_report.csv",
"{OUTDIR}/{project}/Toxin_gene_library_{input_file}_report.tsv"
],
OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]
)
elif w is 'Vir': elif w is 'Vir':
include: include:
"workflows/Virulence_workflow" "workflows/Virulence_workflow"
rule all: rule all:
input: input:
expand("{OUTDIR}/{project}/Virulence_prediction_{input_file}_report.csv", expand(
OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]) "{OUTDIR}/{project}/Virulence_prediction_{input_file}_report.csv",
OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]
)
elif w is 'AMR': elif w is 'AMR':
include: include:
"workflows/AMR_workflow" "workflows/AMR_workflow"
rule all: rule all:
input: input:
expand(["{OUTDIR}/{project}/AMR_MGE_prediction_{input_file}_report.tsv", expand(
"{OUTDIR}/{project}/AMR/{input_file}_AMR_MGE_prediction_detailed.tsv"], [
OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]) "{OUTDIR}/{project}/AMR_MGE_prediction_{input_file}_report.tsv",
"{OUTDIR}/{project}/AMR/{input_file}_AMR_MGE_prediction_detailed.tsv"
],
OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]
)
else: else:
raise Exception('NO workflow selected') raise Exception('NO workflow selected')
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