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etransafe-text-mining-pipeline
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INB
eTRANSAFE
etransafe-text-mining-pipeline
Commits
0b4f5d04
Commit
0b4f5d04
authored
Sep 28, 2020
by
jcorvi
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Update run_gitlab-runner.sh
parent
77c0cffe
Pipeline
#12380
failed with stage
in 1 second
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run_gitlab-runner.sh
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0b4f5d04
...
...
@@ -23,6 +23,6 @@ db_collection_prefix="dev"`date '+%d-%m-%Y'`
#The complete mongo uri
db_uri
=
"mongodb://"
$db_user
":"
$db_password
"@"
$db_server
":"
$db_port
"/?authSource="
$db_name
"&authMechanism=SCRAM-SHA-1"
echo
$db_uri
#
echo $db_uri
#command
$nextflow_path
run
$pipeline_path
--inputDir
$input_dir
--baseDir
$base_dir
--db_uri
$db_uri
--db_name
$db_name
--db_collection_prefix
$db_collection_prefix
-with-report
$base_dir
/report.html
-with-trace
-with-timeline
$base_dir
/timeline.html
-name
$pipeline_name
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