HistologyPyramidConvert

A Nextflow pipeline that converts standard histology TIFF whole-slide images (WSI) into tiled pyramid TIFFs (OME-style pyramid TIFF), suitable for viewers that expect zoom levels and tiles.

What it does

For each row in the input CSV, the convert_pyramid process runs libvips (vips tiffsave) inside a container and writes a TIFF with:

• Multi-resolution pyramid (--pyramid)
• 256×256 tiles (--tile-width, --tile-height)
• JPEG compression
• Large-file support (--bigtiff)
• Declared resolution 20000 pixels per cm in X and Y (--xres, --yres, --resunit cm)

Outputs are copied to the configured output directory (publishDir). If a task fails, the current strategy is ignore (remaining samples continue).

Requirements

• Nextflow (compatible with this repository’s main.nf)
• Singularity / Apptainer (the local and kutral profiles use the OCI image via Singularity)
• Image: oras://community.wave.seqera.io/library/libvips:8.17.3--73bbb05066bc0731 (set in nextflow.config for convert_pyramid)

Input: CSV

--data must point to a headered CSV that includes a wsi column: path to the input TIFF for each case.

Example:

wsi
/path/to/case1.tif
/path/to/case2.tif

Parameters

Parameter	Description	Default
--data	Path to CSV with wsi column	(required)
--outdir	Published output directory	../HE_pyramid/
--debug	Reserved in config	false

Execution reports (timeline, report, trace, DAG) are written under ${params.outdir}/pipeline_info/ with a timestamp.

Running

Minimal example (adjust profile and paths for your environment):

nextflow run main.nf \
  -profile local \
  --data samples.csv \
  --outdir ./pyramid_output

For the kutral profile in nextflow.config (Slurm, queue ngen-ko, site-specific mounts and cluster options), use -profile kutral instead of local.

Output

• One pyramid TIFF per valid CSV row under --outdir, following the process naming (result/<wsi_basename> as published).
• Nextflow run metadata in pipeline_info/.

Process configuration

In nextflow.config, convert_pyramid is set to 10 GB memory and 1 CPU. Profiles bind /mnt/beegfs/labs/; adjust singularity.runOptions if your data live elsewhere.

License

See the LICENSE file in this repository.