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Parameter reference

Parameters controlling the pipeline behavior

The following parameters control the pipeline as a whole. The details below correspond to the Nextflow usage - Galaxy usage will be similar, but through the GUI interface. These can be specified on the command line using the double-dash format (e.g., --in), or inside a YAML file as key-value pairs. Parameters that don’t require an explicit value because their presence controls the behavior (e.g., --tma) should instead be assigned to true in the YAML file. For example,

Example: nextflow run labsyspharm/mcmicro --in /my/data --tma

or equivalently: nextflow run labsyspharm/mcmicro -params-file myparams.yml, where myparams.yml contains

in: /my/data
tma: true

Required parameters:

ParameterDescription
--in /local/pathLocation of the data

Optional parameters:

ParameterDefaultDescription
--sample-name <myname>Directory name supplied to --inThe name of the experiment/specimen
--start-at <step>registrationName of the first step to be executed by the pipeline. Must be one of illumination, registration, dearray (TMA only), probability-maps, segmentation, quantification, cell-states
--stop-at <step>quantificationName of the final step to be executed by the pipeline. Spans the same vocabulary as --start-at.
--tmaOmittedIf specified, mcmicro treats input data as a TMA. If omitted, the input is assumed to be a whole-slide image.
--ilastik-model <model.ilp>NoneA custom .ilp file to be used as the classifier model for ilastik.
--probability-maps <choice>unmicstWhich module(s) to use for probability map computation. Must be one of unmicst, ilastik, all (unmicst AND ilastik), and cypository for cytoplasm segmentation

Parameters for individual modules

Module-specific parameters can be specified using the various opts arguments, followed by the parameters enclosed inside single quotes ':

Example 1: nextflow run labsyspharm/mcmicro --in /my/data --ashlar-opts '-m 30 --pyramid'

Example 2: nextflow run labsyspharm/mcmicro --in /my/data --nstates-opts '--log no --plots pdf'

Example 3: nextflow run labsyspharm/mcmicro --in /my/data --quant-opts '--masks cytoMask.tif nucleiMask.tif'

Arguments to ASHLAR (--ashlar-opts)

Arguments to Coreograph(--core-opts)

Arguments to UnMicst(--unmicst-opts)

Arguments to S3Segmenter(--s3seg-opts)

Arguments to MCquant(--quant-opts)

For more information about the parameters relevant to each MCMICRO module, see the modules landing page.