Workflow parameters

Parameters under the namespace workflow regulate the function of the pipeline as a whole.

By default, the pipeline starts from the registration step (ASHLAR), proceeds through UnMICST, S3segmenter, and stops after executing the quantification MCQuant step.

start-at

Name of the first step to be executed by the pipeline

• Valid values: illumination, registration, background (background only), 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, background (background only), dearray (TMA only), segmentation, quantification, downstream
• Default: quantification
• Example:

workflow:
  stop-at: downstream

Additional examples: Specifying start and stop modules

Use start-at and stop-at workflow parameters to execute any contiguous section of the pipeline. Remember, by default the pipeline will run from ASHLAR through MCQuant.

Example 1: Running illumination correction and registration only

workflow:
  start-at: illumination
  stop-at: registration

Example 2: Start by dearraying an already-registered TMA image

workflow:
  tma: true
  start-at: dearray

Note: Starting at any step beyond registration requires pre-computed output of the previous steps placed at the correct location in the project directory.

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

segmentation-recyze

Whether the image should be reduced to the channels specified in segmentation-channel prior to being provided to the segmentation modules.

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

workflow:
  segmentation-channel: 5
  segmentation-recyze: true

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, cellpose 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

Whether QC files should be copied, moved, hard linked, or symbolically linked from work directories to the project directory. ‘inherit’ may be specified to use the value of the publish_dir_mode pipeline parameter.

• Valid values: copy, move, link, symlink, inherit
• Default: inherit
• Example:

workflow:
  qc-files: move

background

Whether background subtraction should be performed, and the computed intermediates used in further processing

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

workflow:
  background: true

background-method

Which background subtraction module to use when background: true.

• Valid values: backsub, imagej-rolling-ball
• Default: backsub
• Example:

workflow:
  background-method: backsub