ENCODE-DCC/caper: v1.2.0

Added caper cleanup to clean up outputs of a single workflow.

• Usage:
  • caper cleanup [METADATA_JSON_FILE]: Define a metadata.json file for the first positional argument.
  • caper cleanup [KEYWORD_TO_FIND_WORKFLOW]: Define a keyword to find a workflow from a running caper server.
• This DELETEs ALL FILES on a workflow root directory (under key workflowRoot in metadata JSON) written in metadata. Deletion is done in a rm -rf fashion.
• This action is NOT REVERSIBLE. Use this at your own risk.
• Add --delete to actually delete all outputs. Otherwise, caper cleanup will just dry-run.

Added caper gcp_monitor to monitor resources of workflows run on Google Clouds.

• Usage:
  • caper gcp_monitor [METADATA_JSON_FILE]: Define a metadata.json file for the first positional argument.
  • caper gcp_monitor [KEYWORD_TO_FIND_WORKFLOW]: Define a keyword to find a workflow from a running caper server.
• Output will be either in a TSV format or in a JSON format.
  • TSV: Flatten version (with dot notation) of JSON one.
  • JSON: More detailed.
• This feature is available for a workflow run with Caper>=1.2.0.
• Outputs:
  • Task name / shard index / status / ...
  • Instance resource info: cpu, memory, Cromwell-mounted disk.
  • Statistics of resources: mean, std, min, max of each resource (memory, Cromwell-mounted disk's usage, cpu_pct).