Commit a2bf870d authored by jcorvi's avatar jcorvi

Add new file

parent 2048ce52
Pipeline #12367 failed with stage
in 3 minutes and 1 second
#!/bin/bash
#set pipeline name
pipeline_name=pretox_pipeline_`date '+%d-%m-%Y_%H_%M_%S'`
#set the nextflow instalation
nextflow_path="/home/jcorvi/nextflow_installation/nextflow"
#set the pipeline file
pipeline_path="/home/jcorvi/projects/etransafe/etransafe-text-mining-pipeline/pipeline.nf"
#set the input dir
input_dir="/home/jcorvi/eTRANSAFE_DATA/workshop_data/gitlab-ci/input/"
#set the home/work dir of the pipeline
base_dir="/home/jcorvi/eTRANSAFE_DATA/workshop_data/gitlab-ci/"`date '+%d-%m-%Y'`
echo "prueba de echo y variable de entorno"
echo $db_server
#Database connection details
#set server and port
db_server=xxxx
db_port=xxxxx
#set user and password
db_user=xxxxx
db_password=xxxxx
#set the database name
db_name=xxxxxx
#set the collection prefix
db_collection_prefix=xxxxx
#The complete mongo uri
db_uri="mongodb://"$db_user":"$db_password"@"$db_server":"$db_port"/?authSource="$db_name"&authMechanism=SCRAM-SHA-1"
#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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