Run

Running SIMPLI

SIMPLI is run as a Nextflow pipeline:

nextflow run main.nf [COMMAND_LINE_ARGUMENTS] [NEXTFLOW_OPTIONS]

The most recent version of SIMPLI be downloaded and run from directly from this repository with: nextflow run https://github.com/ciccalab/SIMPLI [COMMAND_LINE_ARGUMENTS] [NEXTFLOW_OPTIONS]

See the Nextflow documentation for more details.

Command Line Parameters

SIMPLI accepts the following command line parameters with default values:

Input

These parameters specify the paths to the four configuration files:

• raw_metadata_file = "$baseDir/example_data/sample_metadata.csv"
• channel_metadata = "$params.data_folder/channel_metadata.csv"
• area_measurements_metadata = "$baseDir/example_data/marker_area_metadata.csv"
• cell_threshold_metadata = "$baseDir/example_data/cell_threshold_metadata.csv"

See the input page for their fields and formatting.

Processing

These parameters specify the paths to the two CellProfiler3 pipeline files used by SIMPLI:

• cp3_preprocessing_cppipe = "single_preprocessing_example.cppipe"
• cp3_segmentation_cppipe = "example_segmentation_pipeline.cppipe"

See the CellProfiler3 pipelines page for the requirements of a SIMPLI compatible CellProfiler3 pipeline.

Visualization

These parameters specify the colors used to generate the gradients representing different levels of gene expression in UMAPs and Heatmaps:

• high_color = "'#FF0000'"
• mid_color = "'#FFFFFF'"
• low_color = "'#0000FF'"

Accepted values are color names or hexadecimal #RGB or #RGBA format ("#RRGGBB" or "#RRGGBBAA").

Output

• output_folder = "$baseDir/example_output"
  Specifies the path where all output will be collected.
• tiff_type = "single" Output the preprocessed images as multiple single channel tiff files, or as a single multichannel .ome.tiff image.

See the output page for details on output paths and formatting.