Add new file

run_gitlab-runner.sh

+#!/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