Skip to content
GitLab
Projects
Groups
Snippets
Help
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Sign in
Toggle navigation
Open sidebar
IMP
IMP
Commits
5baaeed4
Commit
5baaeed4
authored
May 06, 2020
by
Valentina Galata
Browse files
mongoDB.smk: fixed wrong config keywords and a syntax error in a rule msg
parent
1135e829
Changes
1
Hide whitespace changes
Inline
Side-by-side
Showing
1 changed file
with
3 additions
and
3 deletions
+3
-3
workflow/rules/Summary/mongoDB.smk
workflow/rules/Summary/mongoDB.smk
+3
-3
No files found.
workflow/rules/Summary/mongoDB.smk
View file @
5baaeed4
...
@@ -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["
B
inning"]["
B
inners"],
binners = config["
b
inning"]["
b
inners"],
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["
B
inning"]["
B
inners"],
binners = config["
b
inning"]["
b
inners"],
dbs = config["hmm_DBs"],
dbs = config["hmm_DBs"],
user = config["mongo_user"],
user = config["mongo_user"],
password = config["mongo_password"],
password = config["mongo_password"],
...
...
Valentina Galata
@valentina.galata
mentioned in issue
#155 (closed)
·
May 07, 2020
mentioned in issue
#155 (closed)
mentioned in issue #155
Toggle commit list
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment