Running HistoQC¶

Basic Usage¶

A typical command line for running HistoQC looks like:

histoqc -c v2.1 -n 3 "*.svs"

Command Line Interface¶

Run HistoQC main quality control pipeline for digital pathology images

usage: histoqc [-h] [-o OUTDIR] [-p BASEPATH] [-c CONFIG] [-f] [-b BATCH]
               [-s SEED] [-n NPROCESSES] [--symlink TARGET_DIR] [--debug]
               input_pattern [input_pattern ...]

Positional Arguments¶

input_pattern: input filename pattern (try: .svs or target_path/.svs ), or tsv file containing list of files to analyze

Named Arguments¶

-o, --outdir

outputdir, default ./histoqc_output_YYMMDD-hhmmss

Default: './histoqc_output_20251210-230208'

-p, --basepath

base path to add to file names, helps when producing data using existing output file as input

Default: ''

-c, --config

config file to use, either by name supplied by histoqc.config (e.g., v2.1) or filename

-f, --force

force overwriting of existing files

Default: False

-b, --batch

break results file into subsets of this size

-s, --seed

set a seed used to produce a random number in all modules

-n, --nprocesses

number of processes to launch

Default: 1

--symlink

create symlink to outdir in TARGET_DIR

--debug

trigger debugging behavior

Default: False