runscripts.workflow

runscripts.workflow.build_runtime_image(image_name)

runscripts.workflow.build_wcm_image(image_name, runtime_image_name)

runscripts.workflow.copy_to_filesystem(source, dest, filesystem)

Robustly copy the contents of a local source file to a destination path on a PyArrow filesystem.

Parameters:

• source (str) – Path to source file on local filesystem

• dest (str) – Path to destination file on PyArrow filesystem. If Cloud Storage bucket, DO NOT include gs:// or gcs://.

• filesystem (FileSystem) – PyArrow filesystem instantiated from URI of dest

runscripts.workflow.generate_code(config)

runscripts.workflow.generate_colony(seeds)

Create strings to import and compose Nextflow processes for colony sims.

Parameters:

seeds (int)

runscripts.workflow.generate_lineage(seed, n_init_sims, generations, single_daughters, analysis_config)

Create strings to import and compose Nextflow processes for lineage sims: cells that divide for a number of generations but do not interact. Also contains import statements and workflow jobs for analysis scripts.

Parameters:

• seed (int) – First seed for first sim

• n_init_sims (int) – Number of sims to initialize with different seeds

• generations (int) – Number of generations to run for each seed

• single_daughters (bool) – If True, only simulate one daughter cell each gen

• analysis_config (dict[str, dict[str, dict]]) –

  Dictionary with any of the following keys:

  {
      'variant': analyses to run on output of all cells combined,
      'cohort': analyses to run on output grouped by variant,
      'multigen': analyses to run on output grouped by variant & seed,
      'single': analyses to run on output for each individual cell,
      'parca': analyses to run on parameter calculator output
  }
  
  Each key corresponds to a mapping from analysis name (as defined
  in ``ecol/analysis/__init__.py``) to keyword arguments.
  

Returns:

2-element tuple containing

• sim_imports: All include statements for Nextflow sim processes

• sim_workflow: Fully composed workflow for entire lineage

runscripts.workflow.main()