Commit dd21f7e2 authored by Laura Denies's avatar Laura Denies
Browse files

Update Snakefile

parent c33869cf
#Snakefile
Snakefile
w = 'complete'
if w is 'complete':
include:
"workflows/Combine_PathoFact_workflow"
rule all:
input:
expand("{OUTDIR}/{project}/PathoFact_{input_file}_predictions.csv",
OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"])
include:
"workflows/Combine_PathoFact_workflow"
rule all:
input:
expand(["{OUTDIR}/{project}/AMR/{input_file}_AMR_MGE_prediction_detailed.tsv",
"{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':
include:
"workflows/Toxin_workflow"
rule all:
input:
expand(["{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"])
include:
"workflows/Toxin_workflow"
rule all:
input:
expand(["{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':
include:
"workflows/Virulence_workflow"
rule all:
input:
expand("{OUTDIR}/{project}/Virulence_prediction_{input_file}_report.csv",
OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"])
include:
"workflows/Virulence_workflow"
rule all:
input:
expand("{OUTDIR}/{project}/Virulence_prediction_{input_file}_report.csv",
OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"])
elif w is 'AMR':
include:
"workflows/AMR_workflow"
rule all:
input:
expand(["{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"])
include:
"workflows/AMR_workflow"
rule all:
input:
expand(["{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:
raise Exception('NO workflow selected')
raise Exception('NO workflow selected')
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