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export_large_annotation_regions

Nextflow pipeline for exporting large annotation regions from a QuPath project using headless QuPath and a Groovy script.

What it does

  • Runs QuPath in CLI mode against a .qpproj project.
  • Executes export_large_annotation_region.groovy to export selected annotation ROIs.
  • Collects exported OME-TIFF outputs from ExportedAnnotations/.

Required parameters

  • --project Path to QuPath project (.qpproj).
  • --qupath_bin Path to QuPath executable (default: /stornext/System/data/software/rhel/9/base/tools/QuPath/0.6.0/bin/QuPath).

Optional:

  • --script Groovy script path (default: bin/export_large_annotation_region.groovy). Relative paths are resolved from the pipeline directory.
  • --target_annotation_names Comma-separated annotation names (default: annotation_1). Use an empty string ("") to export all annotations.
  • --downsample Export downsample factor (default: 1.0).
  • --compression_type OME-TIFF compression type for QuPath writer (default: LZW).
  • --output_subdir QuPath project-side output subdirectory name (default: ExportedAnnotations).
  • --tile_size OME writer tile width/height in pixels (default: 512).
  • --num_cpus Threads used by QuPath writer parallelization (default: 48).
  • --big_tiff Enable BigTIFF output for large files (default: true).
  • --build_pyramid Enable pyramidal OME-TIFF output (default: true).
  • --outdir Output directory for published results (default: results).
  • --publish_dir_mode Nextflow publishDir mode (default: copy).

Usage

Run on HPC with Slurm resources matching the default medium profile (48 CPUs, 450 GB RAM):

nextflow run main.nf \
	--project /vast/projects/project_name/Qupath_project/project.qpproj \
	--qupath_bin /stornext/System/data/software/rhel/9/base/tools/QuPath/0.6.0/bin/QuPath \
	--script bin/export_large_annotation_region.groovy \
	--target_annotation_names annotation_1,annotation_2 \
	--downsample 1.0 \
	--compression_type LZW \
	--output_subdir ExportedAnnotations \
	--tile_size 512 \
	--num_cpus 48 \
	--big_tiff true \
	--build_pyramid true \
	--outdir /path/to/output

Resource profiles

The pipeline defaults to the standard profile, configured with medium resources.

Profile Executor Queue CPUs (process_heavy) Memory (process_heavy) Time (process_heavy)
standard (default) slurm regular 48 450 GB 24h
small slurm regular 16 128 GB 24h
medium slurm regular 48 450 GB 24h
large slurm regular 64 1200 GB 24h

Use -profile small, -profile medium, or -profile large to override the default resource profile.

Outputs

  • ExportedAnnotations/ containing exported .ome.tif region files.
  • qupath_large_annotation_export.log with full QuPath run logs.

Notes

  • Groovy export settings are now pipeline parameters, so you can change them via CLI without editing the script.
  • If your environment does not provide module load java/17, use a QuPath build that bundles Java or enable the conda profile in nextflow.config.