slideJobChecker - swvanderlaan/slideToolKit GitHub Wiki
slideJobChecker is designed to check the consistency of slideToolKit runs by analyzing error files in a given project directory. The script looks for specific patterns in error files related to different analysis steps and generates readme files summarizing the results.
Usage:
bash slideJobChecker.sh [ARG1] [ARG2] [ARG3] [ARG4]
Example usage:
bash slideJobChecker.sh FIBRIN /path/to/working/directory slide2tiles V1
Argument(s):
ARG1- Name of the stain as it appears in the filenames (e.g.,
FIBRIN). Required.
- Name of the stain as it appears in the filenames (e.g.,
ARG2- Path to the working directory, where all the image subdirectories are. Required.
ARG3- Analysis step to be checked, containing the start of the error file (e.g.,
slidemask,slide2tiles,slidenormalize,slidecellprofiler,slidewrapup). Required.
- Analysis step to be checked, containing the start of the error file (e.g.,
Optional argument(s):
ARG4- Unique label, a string-number combination (no spaces) for reference to the analysis run (optional). Optional.