Update readme

README.md

@@ -5,48 +5,28 @@ A NextFlow pipeline to run image rendering process to generate resources for the
 - Converts bioformats files into OME-TIFF
 - Generates a `story.json` file using [Auto-Minerva](https://github.com/jmuhlich/auto-minerva)
 - Renders a Minerva story using [Minerva Author](https://github.com/labsyspharm/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](https://github.com/adamjtaylor/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).
+- Renders a thumbnail image using [Miniature](https://github.com/adamjtaylor/miniature)
 
 A Docker container ([ghcr.io/sage-bionetworks-workflows/nf-artist](https://github.com/sage-bionetworks-workflows/nf-artist/pkgs/container/nf-artist)) is used to ensure reproducibility.
 
 ## Example usage
 
 ```
-nextflow run ghcr.io/sage-bionetworks-workflows/nf-artist --input_path <path-to-image> --outdir <output-directory> --all
+nextflow run ghcr.io/sage-bionetworks-workflows/nf-artist --input <path-to-samplesheet> --outdir <output-directory>
 ```
 
 ## Options
 
-`--outdir` - output directory. Default: `.`  
-`--minerva`: Renders an [Auto-Minerva](https://github.com/jmuhlich/auto-minerva) story  
-`--miniature` - Renders a thumbnail image using [Miniature](https://github.com/adamjtaylor/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
+`--input` [required] - Path to samplesheet. See samplesheet requirements  
+`--outdir` - Output directory. Default: `outputs`
 
-## Example flow diagram:
+#### Samplesheet requriments
 
-![image](https://user-images.githubusercontent.com/14945787/133272620-18223615-ce22-41c3-807b-3f3007b8f080.png)
+The samplesheet specified in the `input` parameter should be a CSV file with the following columns
 
-## Docker pointers
+- `image`: [string] Path or URI to image to be processed
+- `convert`: [boolean] Should the image be converted to a OME-TIFF
+- `he`: [boolean] Is the image a H&E image
+- `minerva`: [boolean] Should a Minerva story be generated
+- `miniatuee`: [boolean] Should a Miniature thumbnail be generated
 
-### Test docker container
-
-`docker run -ti ghcr.io/sage-bionetworks-workflows/nf-artist`
-
-## Build docker container
-
-`docker build -t ghcr.io/sage-bionetworks-workflows/nf-artist docker/`