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HTAN Artist

🚨 This workflow has been superseded by nf-artist.

A NextFlow piepline to run image rendering process to generate resources for the HTAN Portal.

  • Converts bioformats files into OME-TIFF
  • Generates a story.json file using Auto-Minerva
  • Renders a Minerva story using Minerva Author
  • If the --all parameter is set, renders a thumbnail, an autominerva story and gets the metadata
  • If the --miniature parameter is set, renders a thumbnail image using Miniature
  • --he assumes the channel is a brighfield microscopy image of H&E stained tissue and uses a fixed, unscaled story.json and a custom color legend
  • --input can be the path to an image (with * wildcards) or a csv manifest of cloud storage uris (one per line).

A Docker container (adamjtaylor/htan-artist) is used to ensure reproducibility.

Example usage

nextflow run adamjtaylor/htan-artist --input_path <path-to-image> --outdir <output-directory> --all

Options

--outdir - output directory. Default: .
--minerva: Renders an Auto-Minerva story
--miniature - Renders a thumbnail image using Miniature
--metadata - Extract headers from the image and save as a json
--all - set --minerva --miniature and --metadata
--he - Use an unscaled scene for Minerva story and thumbnail generation. Suitable for H&E images
--input_csv - Path to a csv with a file path, uid, or synapseID per row
--input_synid - A synapse ID
--input_path - The path to a file. Can take wildcards
--watch_path - A path to watch for files that are created or modified
--watch_csv - A path to a csv to watch for if it is modified
--echo - Echo outputs
--keepBg - Keep the background in thumbnails
--level - the pyramid level used in thumbnauls, Default: -1 (highest)
--bioformats2ometiff - Convert images to ome-tiff. Default: true
--synapseconfig - Path to a synapseConfig file. Required for Synapse authentication

Example flow diagram:

image

Docker pointers

Test docker container

docker run -ti adamjtaylor/htan-artist

Build docker container

docker build -t adamjtaylor/htan-artist docker/