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Table of contents
  1. Workflow parameters
    1. start-at
    2. stop-at
    3. tma
    4. segmentation-channel
    5. ilastik-model
    6. segmentation
    7. downstream
    8. viz
    9. qc-files

Workflow parameters

start-at

Name of the first step to be executed by the pipeline

  • Valid values: illumination, registration, dearray (TMA only), segmentation, watershed, quantification, downstream
  • Default: registration
  • Example:
workflow:
  start-at: segmentation

stop-at

Name of the final step to be executed by the pipeline

  • Valid values: illumination, registration, dearray (TMA only), segmentation, quantification, downstream
  • Default: quantification
  • Example:
workflow:
  stop-at: downstream

tma

If true, MCMICRO treats input data as a TMA. If false, the input is assumed to be a whole-slide image

  • Valid values: true, false
  • Default: false
  • Example:
workflow:
  tma: true

segmentation-channel

One or more channels to use for segmentation, specified using 1-based indexing; values will be forwarded to all segmentation modules

  • Valid values: one or more positive integers, each separated with a space
  • Default: 1
  • Example:
workflow:
  segmentation-channel: 1 5

ilastik-model

A custom .ilp file to be used as the classifier model for ilastik

  • Valid values: A full path to any file
  • Default: None
  • Example:
workflow:
  ilastik-model: /full/path/to/mymodel.ilp

segmentation

A list of segmentation modules to run

  • Valid values: One or more of unmicst, ilastik, mesmer, cypository, specified as a YAML list
  • Default: unmicst
  • Example:
workflow:
  segmentation: [unmicst, ilastik]

downstream

A list of downstream modules to run

  • Valid values: One or more of naivestates, scimap, fastpg, scanpy, flowsom
  • Default: scimap
  • Example:
workflow:
  downstream: [scanpy, flowsom]

viz

Whether to generate a vizualization with Auto-Minerva

  • Valid values: true, false
  • Default: false
  • Example:
workflow:
  viz: true

qc-files

Wheter QC files should be copied, moved or symbolically linked from work directories to the project directory

  • Valid values: copy, move, symlink
  • Default: copy
  • Example:
workflow:
  qc-files: move