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 metadata 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:

• cp4_preprocessing_cppipe = "single_preprocessing_example.cppipe"
• cp4_segmentation_cppipe = "example_segmentation_pipeline.cppipe"

See the CellProfiler4 pipelines page for the requirements of a SIMPLI compatible CellProfiler4 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.

Configuration file

In alternative all command line parameters can be specified through a configuration file: nextflow run main.nf -c CONFIGURATION_FILE

Parameters in the configuration file are specified in this format:

params.output_folder ="VALUE"                                                                         
params.channel_metadata = "VALUE"                                         
params.raw_metadata_file = "VALUE"                                         
params.tiff_type = "single"                                                                                             
params.cp4_preprocessing_cppipe = "VALUE"                                 
params.cp4_segmentation_cppipe = "VALUE"                              
params.area_measurements_metadata = "VALUE"                           
params.cell_analysis_metadata = "VALUE"                                                                                                                                         params.high_color = "VALUE"                                                                                         
params.mid_color = "VALUE"                                                                                         
params.low_color = "VALUE" 

Colors in hexadecimal format should be double quoted like this "'#0000FF'".