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GitLab CI/CD

This document outlines the environment variables that must be provided in GitLab CI/CD for the pipeline to function correctly. These variables should be configured in the GitLab repository settings under Settings > CI/CD > Variables.

Required Environment Variables

Variable Name Description
API_ENDPOINT_FILE_DOWNLOADS_PER_FILE API endpoint for updating file-level download statistics.
API_ENDPOINT_FILE_DOWNLOADS_PER_PROJECT API endpoint for updating project-level download statistics.
API_ENDPOINT_HEADER Authorization header for API requests.
CONDA_INIT Path to the Conda initialization script.
DATA_ROOT_DIR Root directory where data is stored.
DEPLOY_PATH Path where the pipeline artifacts or results will be deployed.
DEPLOY_SERVER The server address where deployment occurs.
LOG_FOLDER Directory where logs should be stored.
NEXTFLOW Path to the Nextflow executable.
PIPELINE_BASE_DIR Base directory of the pipeline execution.
SERVER_USER Username for the deployment server.
SSH_KEY SSH private key for accessing the deployment server.
SYMLINK Path to create symbolic links for processed data.
WORK_PATH Working directory for pipeline execution.

Setting Up Variables in GitLab CI/CD

To configure these variables:
1. Navigate to your GitLab project.
2. Go to Settings > CI/CD.
3. Expand the Variables section.
4. Click Add Variable and enter the name, value, and choose the appropriate scope and protection.
5. Click Save variables.

.gitlab-ci.yml

Ensure that your .gitlab-ci.yml file references these variables correctly

Security Recommendations

  • Protect sensitive variables (SSH_KEY, API_ENDPOINT_HEADER) by marking them as protected and masked.
  • Avoid exposing secrets in logs by setting Mask Variable when adding them to GitLab CI/CD.
  • Use SSH keys securely by ensuring SSH_KEY is configured correctly for authentication.

Troubleshooting

If any variable is missing or incorrectly set, the pipeline may fail. Check the following:

  • Ensure all required variables are defined in Settings > CI/CD > Variables.
  • Use echo $VARIABLE_NAME in the pipeline script to debug missing variables.
  • Check GitLab CI/CD logs for any environment variable errors.