opal_inform_stitch

Nextflow pipeline for stitching Opal/inForm images from Vectra Polaris in parallel.

Each subdirectory under --base_dir is processed as an independent SLURM job, allowing all slides to be stitched concurrently.

Requirements

• Nextflow ≥ 24.04.2
• conda or mamba (for environment management)

Input structure

base_dir/
    slide_A/
        SlideA_[x,y]_component_data.tif
        ...
    slide_B/
        SlideB_[x,y]_component_data.tif
        ...

Each subdirectory must contain component_data TIFF tiles exported from inForm.

Usage

nextflow run main.nf \
    --base_dir /path/to/slides \
    --outdir /path/to/output \
    -profile conda,large

Profiles

Profile	Memory per job	Target nodes	Use case
small	96 GB	sml (113 GB)	Small slides / test runs
medium	240 GB	med/il (491 GB)	Medium slides
large	960 GB	lrg (1498 GB)	Full-size Vectra Polaris

Combine with a container/environment profile (conda, mamba, singularity, apptainer):

-profile conda,large

Output

Stitched pyramidal OME-TIFF files are written to --outdir:

outdir/
    <sample>_<label>.ome.tif
    pipeline_info/
        execution_timeline_*.html
        execution_report_*.html
        execution_trace_*.txt

Parameters

Parameter	Required	Default	Description
--base_dir	Yes	—	Directory containing one subdirectory per slide
--outdir	Yes	—	Output directory for stitched OME-TIFFs
--publish_dir_mode	No	copy	Nextflow publishDir mode