cellprofiler-nf

A nextflow pipeline to run CellProfiler pipelines on raw images and process output

Pipeline overview

QUEST usage

# clone the repo
git clone https://github.com/AndersenLab/cellprofiler-nf.git
cd cellprofiler-nf

# setup environment
module load python/anaconda3.6
module load singularity
source activate /projects/b1059/software/conda_envs/nf20_env/

# example run with dauer pipeline parameter
nextflow run main.nf --pipeline dauer --project <your repo path>/debug/20220501_dauerDebug

# example run with toxin pipeline parameter
nextflow run main.nf --pipeline toxin --project <your repo path>/debug/20220501_toxinDebug

cellprofiler-nf help

C E L L P R O F I L E R - N F   P I P E L I N E
===============================================
Usage:
The typical command for running the pipeline is as follows:
nextflow run main.nf --pipeline <CellProfiler pipeline to use> --project <path to your project directory>

Mandatory arguments:
--project                      The path to your project directory
--pipeline                     The CP pipeline to use: toxin, dauer

Optional arguments:
--groups                       comma separated metadata groupings for CellProfiler, default is plate,well
--outdir                       Output directory to place files, default is project/Analysis-{current date}
--help                         This usage statement.

Input directory structure

cellprofiler-nf requires that the input project directory contains a raw_images subdirectory that holds all the images to be processed by CellProfiler. See the examples below for dauer and toxin projects. The AndersenLab/easyXpress R package can be used to help organize image files exported from the imager into the required directory structure. See easyXpress::tidyProject for details.

dauer input

20220501_dauerDebug/
├── raw_images
    └── 20220501_dauerDebug-p002-m2X_A01_w1.TIF
    └── 20220501_dauerDebug-p002-m2X_A01_w2.TIF
    └── ...

toxin input

20220501_toxinDebug/
├── raw_images
    └── 20220501_toxinDebug-p001-m2X_A01.TIF
    └── 20220501_toxinDebug-p010-m2X_A01.TIF
    └── 20220501_toxinDebug-p169-m2X_D11.TIF
    └── ...

The files in the raw_image subdirectory must conform to the folloing naming conventions:
| dauer - Date-Experiment Name-Plate-Magnification_Well_Wavelength.TIF
| toxin - Date-Experiment Name-Plate-Magnification_Well.TIF

Output directory structure

By default cellprofiler-nf will output results to a subdirectory in the project folder named Analysis-{current date} with the following directory structures.

dauer output

20220501_dauerDebug/
├── raw_images
├── Analysis-{current date}
    └── pipeline
    └── metadata
    └── groups
    └── processed_data
        └── 20220501_dauerDebug_Analysis-{current date}.RData
    └── processed_images
        └── 20220501_dauerDebug-p002-m2X_A01_w1_overlay.png
        └── 20220501_dauerDebug-p002-m2X_A01_w1_dauerMod_straightened_RFP.png
        └── 20220501_dauerDebug-p002-m2X_A01_w1_nondauerMod_straightened_RFP.png
        └── 20220501_dauerDebug-p002-m2X_A01_w2_dauerMod_NonOverlappingWorms_RFP_mask.png
        └── 20220501_dauerDebug-p002-m2X_A01_w2_nondauerMod_NonOverlappingWorms_RFP_mask.png
        └── ...

toxin output

20220501_toxinDebug/
├── raw_images
├── Analysis-{current date}
    └── pipeline
    └── metadata
    └── groups
    └── processed_data
        └── 20220501_toxinDebug_Analysis-{current date}.RData
    └── processed_images
        └── 20220501_dauerDebug-p002-m2X_A01_w1_overlay.png
        └── ...

bkohrn/cellprofiler-nf