Attention

These docs have moved. The current simpleaf documentation lives at https://combine-lab.github.io/simpleaf and is the only version that is updated. This readthedocs site is a frozen snapshot of the 0.27.0 docs and will not track later releases.

simpleaf workflow commands

The simpleaf workflow program exposes a number of different commands that are responsible for exposing different capabilities. The list of current and valid commands are documented below.

Besides, we also provides a simpleaf workflow utility library for developers, which contains useful functions for workflow template development. The simpleaf team has been continously improving existing functions and adding new funtion into this library. The codebase is included in protocol esturary.

• simpleaf workflow get
  • Providing information in workflow configuration file
  • Get Usage
• simpleaf workflow run
  • Workflow Output
  • workflow run: Full Usage
  • The procedure of parsing a simpleaf workflow template
  • Valid simpleaf workflow manifest format
• simpleaf workflow list
  • List Usage
• simpleaf workflow patch
  • Patch file
    • workflow patch: Full Usage
• simpleaf workflow refresh
  • Refresh Usage
• Simpleaf workflow utility library
  • Import the utility library
  • utils.ref_type(o)
  • utils.simpleaf_index(step, ref_type, arguments, output)
  • utils.map_type(o, simpleaf_index = {})
  • utils.cell_filt_type(o)
  • simpleaf_quant(step, map_type, cell_filt_type, arguments, output)
  • feature_barcode_ref(start_step, csv, name_col, barcode_col, output)
  • barcode_translation(start_step, url, quant_cb, output)
  • utils.get(o, f, use_default = false, default = null)