nextflow.py

nextflow.py is a Python wrapper around the Nextflow pipeline framework. It lets you run Nextflow pipelines from Python code.

Example

>>> import nextflow
>>> execution = nextflow.run("main.nf", params={"param1": "123"})
>>> print(execution.status)

Table of Contents

• Installing
  • pip
  • Development
  • Nextflow
  • Testing
• Overview
  • Running
  • Custom Runners
  • Polling
  • Executions
• Full API
  • nextflow.models
    • Execution
      • Execution.duration
      • Execution.status
    • ProcessExecution
      • ProcessExecution.all_output_data()
      • ProcessExecution.duration
      • ProcessExecution.full_path
      • ProcessExecution.input_data()
  • nextflow.command
    • get_execution()
    • get_process_execution()
    • get_process_executions()
    • make_nextflow_command()
    • make_nextflow_command_config_string()
    • make_nextflow_command_env_string()
    • make_nextflow_command_log_string()
    • make_nextflow_command_params_string()
    • make_nextflow_command_profiles_string()
    • make_reports_string()
    • run()
    • run_and_poll()
  • nextflow.log
    • get_datetime_from_line()
    • get_finished_from_log()
    • get_process_end_from_log()
    • get_process_name_from_log()
    • get_process_start_from_log()
    • get_process_status_from_log()
    • get_started_from_log()
    • log_is_finished()
  • nextflow.io
    • get_file_text()
    • get_process_ids_to_paths()
• Changelog
  • Release 0.8.1
  • Release 0.8.0
  • Release 0.7.1
  • Release 0.7.0
  • Release 0.6.2
  • Release 0.6.1
  • Release 0.6.0
  • Release 0.5.0
  • Release 0.4.2
  • Release 0.4.1
  • Release 0.4.0
  • Release 0.3.1
  • Release 0.3
  • Release 0.2.2
  • Release 0.2.1
  • Release 0.2
  • Release 0.1.4
  • Release 0.1.3
  • Release 0.1.2
  • Release 0.1.1
  • Release 0.1