Commit 5baaeed4 authored by Valentina Galata's avatar Valentina Galata
Browse files

mongoDB.smk: fixed wrong config keywords and a syntax error in a rule msg

parent 1135e829
...@@ -30,7 +30,7 @@ rule shut_mongo: ...@@ -30,7 +30,7 @@ rule shut_mongo:
touch("status/DB_filling.done") touch("status/DB_filling.done")
params: params:
port = config["mongo_port"], port = config["mongo_port"],
message: "shut_mongo: killing mongod on config["mongo_port"]." message: "shut_mongo: killing mongod on {port}.".format(port=config["mongo_port"])
shell: shell:
""" """
mongod --dbpath {input[0]} --port {params.port} --shutdown mongod --dbpath {input[0]} --port {params.port} --shutdown
...@@ -56,7 +56,7 @@ rule mongoDB_bins: ...@@ -56,7 +56,7 @@ rule mongoDB_bins:
params: params:
ass = ASS, ass = ASS,
sample = SAMPLE, sample = SAMPLE,
binners = config["Binning"]["Binners"], binners = config["binning"]["binners"],
dbs = config["hmm_DBs"], dbs = config["hmm_DBs"],
user = config["mongo_user"], user = config["mongo_user"],
password = config["mongo_password"], password = config["mongo_password"],
...@@ -79,7 +79,7 @@ rule mongoDB_contigs: ...@@ -79,7 +79,7 @@ rule mongoDB_contigs:
params: params:
ass = ASS, ass = ASS,
sample = SAMPLE, sample = SAMPLE,
binners = config["Binning"]["Binners"], binners = config["binning"]["binners"],
dbs = config["hmm_DBs"], dbs = config["hmm_DBs"],
user = config["mongo_user"], user = config["mongo_user"],
password = config["mongo_password"], password = config["mongo_password"],
......
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