Workflow and task management for genomics research

wftools is a command line tool and package for managing genomics data processing workflows. It communicate with workflows and tasks execution servers through the following APIs:

• Cromwell
• Workflow Execution Service (WES)
• Task Execution Service (TES)

wftools

Usage: wftools [OPTIONS] COMMAND [ARGS]...

  Workflow and task management for genomics research

Options:
  --help  Show this message and exit.

Commands:
  cromwell  Cromwell
  tes       Task Execution Schema
  wes       Workflow Execution Schema

Cromwell commands

• abort Abort a running workflow
• collect Copy or move output files to directory
• describe Describe a workflow
• info Ger server info
• list List workflows
• logs Get the logs for a workflow
• outputs Get the outputs for a workflow
• release Switch from 'On Hold' to 'Submitted' status
• status Retrieves the current state for a workflow
• submit Submit a workflow for execution
• validate Validate a workflow and its inputs
• version Return the version of this Cromwell server

Set CROMWELL_SERVER environment variable to omit --host argument.

export CROMWELL_SERVER=http://localhost:8000
wftools cromwell info

TES commands

• abort Abort a running task
• info Information about the service
• list List tasks
• status Retrieves the current state of a task

Set TES_SERVER environment variable to omit --host argument.

export TES_SERVER=http://localhost:8000
wftools tes info

WES commands

• abort Cancel a running workflow
• info Get information about service
• list List the workflow runs
• logs Get detailed info about a workflow run
• status Get quick status info about a workflow run
• submit Run a workflow

Set WES_SERVER environment variable to omit --host argument.

export WES_SERVER=http://localhost:8000
wftools wes info