diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 15e89de..f862389 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -3,54 +3,54 @@ name: ci
 on:
   push:
     branches:
-     - 'main'
+      - "main"
     paths:
-     - 'docker/**'
-     - '.github/workflows/ci.yml'
+      - "docker/**"
+      - ".github/workflows/ci.yml"
 
 env:
   REGISTRY: ghcr.io
 
 jobs:
-      docker:
-        runs-on: ubuntu-latest
-        permissions:
-          contents: read
-          packages: write
-          id-token: write
-
-        defaults:
-          run:
-            working-directory: './docker'
-
-        steps:
-          - name: Checkout GitHub Action
-            uses: actions/checkout@v3
-
-          - name: Login to GitHub Container Registry (GHCR)
-            uses: docker/login-action@v2
-            with:
-              registry: ${{ env.REGISTRY }}
-              username: ${{ github.actor }}
-              password: ${{ secrets.GITHUB_TOKEN }}
-              
-          - name: Extract Docker metadata
-            id: metadata
-            uses: docker/metadata-action@v4
-            with:
-              images: ${{ env.REGISTRY }}/${{ github.repository }}
-              tags: |
-                type=semver,pattern={{version}}
-                type=semver,pattern={{major}}.{{minor}} 
-                type=semver,pattern={{major}}
-                type=ref,event=branch
-                type=sha
-                latest
-
-          - name: Build and push to GHCR
-            uses: docker/build-push-action@v4
-            with:
-              context: ./docker
-              push: true
-              tags: ${{ steps.metadata.outputs.tags }}
-              labels: ${{ steps.metadata.outputs.labels }}
+  docker:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+      id-token: write
+
+    defaults:
+      run:
+        working-directory: "./docker"
+
+    steps:
+      - name: Checkout GitHub Action
+        uses: actions/checkout@v3
+
+      - name: Login to GitHub Container Registry (GHCR)
+        uses: docker/login-action@v2
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract Docker metadata
+        id: metadata
+        uses: docker/metadata-action@v4
+        with:
+          images: ${{ env.REGISTRY }}/${{ github.repository }}
+          tags: |
+            type=semver,pattern={{version}}
+            type=semver,pattern={{major}}.{{minor}} 
+            type=semver,pattern={{major}}
+            type=ref,event=branch
+            type=sha
+            latest
+
+      - name: Build and push to GHCR
+        uses: docker/build-push-action@v4
+        with:
+          context: ./docker
+          push: true
+          tags: ${{ steps.metadata.outputs.tags }}
+          labels: ${{ steps.metadata.outputs.labels }}
diff --git a/.github/workflows/scan-images.yml b/.github/workflows/scan-images.yml
index 2faa536..c0d73f7 100644
--- a/.github/workflows/scan-images.yml
+++ b/.github/workflows/scan-images.yml
@@ -1,22 +1,22 @@
 name: Scan image
 
 on:
-    push:
-      branches: [ "main" ]
-    pull_request:
-      branches: [ "main" ]
-    schedule:
-      - cron: '32 12 * * 2' # every tuesday at 12:32 UTC time
+  push:
+    branches: ["main"]
+  pull_request:
+    branches: ["main"]
+  schedule:
+    - cron: "32 12 * * 2" # every tuesday at 12:32 UTC time
 
 env:
-    REGISTRY: ghcr.io
-    IMAGE_TAG: latest # scan just latest image
+  REGISTRY: ghcr.io
+  IMAGE_TAG: latest # scan just latest image
 
 jobs:
   trivy:
-    name:  Run Trivy vulnerability scanner
+    name: Run Trivy vulnerability scanner
     permissions:
-        security-events: write # for github/codeql-action/upload-sarif to upload SARIF results
+      security-events: write # for github/codeql-action/upload-sarif to upload SARIF results
     runs-on: ubuntu-latest
 
     steps:
@@ -31,8 +31,8 @@ jobs:
         id: metadata
         uses: docker/metadata-action@v4
         with:
-            images: ${{ env.REGISTRY }}/${{ github.repository }}
-            tags: ${{ env.IMAGE_TAG }}
+          images: ${{ env.REGISTRY }}/${{ github.repository }}
+          tags: ${{ env.IMAGE_TAG }}
 
       - name: Pull the image
         run: |
@@ -43,7 +43,7 @@ jobs:
         with:
           image-ref: ${{ steps.metadata.outputs.tags }}
           ignore-unfixed: true
-          severity: 'CRITICAL,HIGH'
+          severity: "CRITICAL,HIGH"
           limit-severities-for-sarif: true
           format: sarif
           output: trivy-results.sarif
diff --git a/.gitignore b/.gitignore
index 554f083..23227d6 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,4 +3,5 @@ work/
 .nextflow.log*
 test-outputs/
 flowchart*
-outputs/*
\ No newline at end of file
+outputs/*
+.DS_Store
\ No newline at end of file
diff --git a/README.md b/README.md
index 50b82d0..5c2d0d1 100644
--- a/README.md
+++ b/README.md
@@ -3,50 +3,68 @@
 A NextFlow pipeline to run image rendering process to generate resources for the [HTAN Portal](https://github.com/ncihtan/htan-portal).
 
 - Converts bioformats files into OME-TIFF
-- Generates a `story.json` file using [Auto-Minerva](https://github.com/jmuhlich/auto-minerva)
+- Sets thresholds for each channel and pepares 4-channel overlay groups 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>
+```
+
+
+## Output
+
+`nf-artist` outputs the following directory structure into the specified output directory (`outdir`):
+
+```
+├── outdir
+│   ├── <simpleName or id for first row of samplesheet>
+│   │   ├── thumbnail.jpeg
+│   │   ├── minerva
+│   │   │   ├── index.html
+│   │   │   ├── exhibit.json
+│   │   │   ├── story.json
+│   │   │   ├── Group-1
+│   │   │   │   ├── tile1.jpeg
+│   │   │   │   ├── ...
+│   │   │   ├── Group-<n>
+│   │   │   │   ├── tile1.jpeg
+│   │   │   │   ├── ...
+│   ├── < simpleName or id for n'th row of samplesheet>
 ```
 
 ## 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/Output Options:
+
+* **input**: Path to a CSV sample sheet. This parameter is required. (Type: String)
+
+* **outdir**: Specifies the directory where the output data should be saved. Default is "outputs". (Type: String)
+
+#### Miniature Options:
+
+* **remove_bg**: Setting this to true will remove the non-tissue background. Default is true. (Type: Boolean)
+
+* **level**: Specifies the pyramid level used in thumbnails. Default is -1 (smallest). (Type: Integer)
 
-## Example flow diagram:
+* **dimred**: The dimensionality reduction method used. Default is "umap". Options include "umap", "tsne", and "pca". (Type: String)
 
-![image](https://user-images.githubusercontent.com/14945787/133272620-18223615-ce22-41c3-807b-3f3007b8f080.png)
+* **colormap**: Specifies the colormap used. Ensure the colormap is compatible with the number of `n_components` selected. Default is "UCIE". 3D colormap options: "UCIE", "LAB", "RGB". 2D colormap options: "BREMM", "SCHUMANN", "STEIGER", "TEULING2", "ZIEGLER", "CUBEDIAGONAL". (Type: String)
 
-## Docker pointers
+* **n_components**: Specifies the number of components. Default is 3. Options are 2 and 3. (Type: Integer)
 
-### Test docker container
+#### Samplesheet requirements
 
-`docker run -ti ghcr.io/sage-bionetworks-workflows/nf-artist`
+The samplesheet specified in the `input` parameter should be a CSV file with the following columns
 
-## Build docker container
+- `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
+- `id`: *optional* [string] A custom identifier to replace image simpleName in output directory structure 
 
-`docker build -t ghcr.io/sage-bionetworks-workflows/nf-artist docker/`
diff --git a/TODO.md b/TODO.md
new file mode 100644
index 0000000..f2bb1e0
--- /dev/null
+++ b/TODO.md
@@ -0,0 +1,14 @@
+# nf-artist
+nf-artist is a Nextflow pipeline to generate interactive multiplexed image explorations and thumbnails.
+
+- Add CI testing in Github action using included test data in `data/` and samplesheet `data/test_samplesheet.csv`
+- Move logic on if minerva story or miniature thumbnail are run out of samplesheet and into `params`
+
+## Minerva
+- ✅ ~~Ensure H&E images are rendered with a fixed legend~~
+- Allow for custom descriptions to be provided in the samplesheet and added into the Minerva story
+- Update to new version of Minerva with channel selection
+
+## Miniature
+
+- Split `make_miniature` into two processes, one to run the miniature script for multiplexed images and one (that can have lower resource requirements) that makes the brightfield thumbnail for H&E images with TiffSlide
\ No newline at end of file
diff --git a/assets/he_story.json b/assets/he_story.json
new file mode 100644
index 0000000..175ccd6
--- /dev/null
+++ b/assets/he_story.json
@@ -0,0 +1,21 @@
+{
+  "sample_info": {
+    "name": "",
+    "rotation": 0,
+    "text": "",
+    "pixels_per_micron": null
+  },
+  "defaults": [],
+  "groups": [
+    {
+      "label": "H&E",
+      "channels": [
+        { "color": "ffffff", "id": 0, "label": "H&E", "min": 0, "max": 1 }
+      ],
+      "render": [
+        { "color": "ffffff", "id": 0, "label": "H&E", "min": 0, "max": 1 }
+      ]
+    }
+  ],
+  "waypoints": []
+}
diff --git a/data/CMU-1-Small-Region.svs b/data/CMU-1-Small-Region.svs
new file mode 100644
index 0000000..1125dcd
Binary files /dev/null and b/data/CMU-1-Small-Region.svs differ
diff --git a/data/cycif_tonsil_small.tiff b/data/cycif_tonsil_small.tiff
deleted file mode 100644
index b64d934..0000000
Binary files a/data/cycif_tonsil_small.tiff and /dev/null differ
diff --git a/data/cycif_tonsil_very_small.ome.tiff b/data/cycif_tonsil_very_small.ome.tiff
deleted file mode 100644
index 62db5a8..0000000
Binary files a/data/cycif_tonsil_very_small.ome.tiff and /dev/null differ
diff --git a/data/exemplar-001_small.tif b/data/exemplar-001_small.tif
new file mode 100644
index 0000000..4b5a24e
Binary files /dev/null and b/data/exemplar-001_small.tif differ
diff --git a/data/test.csv b/data/test.csv
deleted file mode 100644
index 04161e3..0000000
--- a/data/test.csv
+++ /dev/null
@@ -1,2 +0,0 @@
-image,he
-data/cycif_tonsil_very_small.ome.tiff, false
\ No newline at end of file
diff --git a/data/test_samplesheet.csv b/data/test_samplesheet.csv
new file mode 100644
index 0000000..641e932
--- /dev/null
+++ b/data/test_samplesheet.csv
@@ -0,0 +1,3 @@
+image,convert,he,minerva,miniature,id
+datas/exemplar-001_small.tif,true,false,true,true,cycif
+data/CMU-1-Small-Region.svs,true,true,true,true,h_and_e
\ No newline at end of file
diff --git a/docker/Dockerfile b/docker/Dockerfile
index 2bdd127..70da05d 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -24,7 +24,6 @@ RUN conda-pack -n artist -o /tmp/env.tar && \
 # so now fix up paths:
 RUN /venv/bin/conda-unpack
 
-
 # The runtime-stage image; we can use Debian as the
 # base image since the Conda env also includes Python
 # for us.
@@ -48,14 +47,9 @@ RUN apt-get update && apt-get install --yes --no-install-recommends \
     libblosc1
 
 RUN source /venv/bin/activate && \
-    #git clone https://github.com/adamjtaylor/miniature.git && \
     git clone https://github.com/adamjtaylor/miniature.git -b v2 && \
-    #git clone https://github.com/jmuhlich/auto-minerva.git && \
     git clone https://github.com/adamjtaylor/auto-minerva.git -b minerva1point5 && \
-    git clone https://github.com/labsyspharm/minerva-author.git minerva-author-dev && \
-    git clone https://github.com/labsyspharm/minerva-author.git -b v1.11.2 &&  \
-    git clone https://github.com/ncihtan/image-header-validation && \
-    wget https://gist.githubusercontent.com/adamjtaylor/964e206bf1e6f302f6e512082e953193/raw/0acdea0736a027a260a0bb598f619552ff106758/index.html && \
+    git clone https://github.com/labsyspharm/minerva-author.git -b v1.14.0 &&  \
     pip install git+https://github.com/labsyspharm/minerva-lib-python@master#egg=minerva-lib && \
     pip install openslide-python && \
     pip install opencv-python-headless \
diff --git a/docker/environment.yml b/docker/environment.yml
index d0b38e7..df9f387 100644
--- a/docker/environment.yml
+++ b/docker/environment.yml
@@ -31,4 +31,4 @@ dependencies:
   - imagemagick
   - tiffslide=2.1.2
   - libvips
-  - estimagic
\ No newline at end of file
+  - estimagic
diff --git a/main.nf b/main.nf
index bd77000..c938f01 100644
--- a/main.nf
+++ b/main.nf
@@ -12,12 +12,6 @@ params.dimred = "umap"
 params.colormap = "UCIE"
 params.n_components = 3
 
-// made these into params so that they can be accessed anywhere in the pipeline
-// can be added to profiles or other configuration later
-params.heStory = 'https://gist.githubusercontent.com/adamjtaylor/3494d806563d71c34c3ab45d75794dde/raw/d72e922bc8be3298ebe8717ad2b95eef26e0837b/unscaled.story.json'
-params.heScript = 'https://gist.githubusercontent.com/adamjtaylor/bbadf5aa4beef9aa1d1a50d76e2c5bec/raw/1f6e79ab94419e27988777343fa2c345a18c5b1b/fix_he_exhibit.py'
-params.minerva_description_script = 'https://gist.githubusercontent.com/adamjtaylor/e51873a801fee39f1f1efa978e2b5e44/raw/c03d0e09ec58e4c391f5ce4ca4183abca790f2a2/inject_description.py'
-
 include { ARTIST } from './workflows/artist.nf'
 
 workflow NF_ARTIST {
diff --git a/modules/autominerva_story.nf b/modules/autominerva_story.nf
index fab3f04..9d48048 100644
--- a/modules/autominerva_story.nf
+++ b/modules/autominerva_story.nf
@@ -1,23 +1,19 @@
 process autominerva_story {
+  tag {"$meta.id"}
+  label "process_low"
   input:
       tuple val(meta), file(image) 
   output:
       tuple val(meta), file(image), file('story.json')
   publishDir "$params.outdir/$workflow.runName",
-    pattern: 'story.json',
-    saveAs: {filename -> "${meta.id}/$workflow.runName/story.json"}
+      pattern: 'story.json',
+      saveAs: {filename -> "${meta.id}/$workflow.runName/story.json"}
   stub: 
   """
   touch story.json
   """
   script:
-  if (meta.he) {
-    """
-    wget -O story.json $params.heStory
-    """
-  } else {
-    """
-    python3 /auto-minerva/story.py $image > 'story.json'
-    """
-  }
+  """
+  python3 /auto-minerva/story.py $image > 'story.json'
+  """
 }
diff --git a/modules/bioformats2ometiff.nf b/modules/bioformats2ometiff.nf
index e13b43d..2615907 100644
--- a/modules/bioformats2ometiff.nf
+++ b/modules/bioformats2ometiff.nf
@@ -1,4 +1,5 @@
 process bioformats2ometiff {
+  tag {"$meta.id"}
   label "process_medium"
   input:
       tuple val(meta), file(image) 
diff --git a/modules/make_miniature.nf b/modules/make_miniature.nf
index 8999e16..83e2927 100644
--- a/modules/make_miniature.nf
+++ b/modules/make_miniature.nf
@@ -1,5 +1,6 @@
 process make_miniature {
-  label "process_medium"
+  tag {"$meta.id"}
+  label "process_high"
   input:
       tuple val(meta), file(image) 
   output:
diff --git a/modules/minerva.nf b/modules/minerva.nf
deleted file mode 100644
index 6636fe5..0000000
--- a/modules/minerva.nf
+++ /dev/null
@@ -1,93 +0,0 @@
-
-process STORY {
-    label "process_medium"
-    publishDir "$params.outdir/$workflow.runName"
-        mode: 'copy'
-    
-    echo params.echo
-    
-    when:
-        params.minerva == true || params.all == true
-    
-    input:
-        tuple val(synid), file(ome)
-    
-    output:
-        tuple val(synid), file('story.json'), file(ome)
-    
-    stub:
-    """
-    touch story.json
-    """
-    
-    script:
-    """
-    python3 /auto-minerva/story.py $ome > 'story.json'
-    """
-}
-
-
-process RENDER {
-    label "process_medium"
-    publishDir "$params.outdir/$workflow.runName",
-        mode: 'move' 
-    
-    echo params.echo
-    
-    input:
-        tuple (val); synid, file(story), file(ome)
-        file synapseconfig from synapseconfig
-    
-    output:
-        file 'minerva'
-    
-    stub:
-    """
-    mkdir minerva
-    touch minerva/index.html
-    touch minerva/exhibit.json
-    """
-    
-    script:
-    """
-    python3  /minerva-author/src/save_exhibit_pyramid.py $ome $story 'minerva'
-    cp /index.html minerva
-    wget -O inject_description.py $params.minerva_description_script
-    python3 inject_description.py minerva/exhibit.json --synid $synid --output minerva/exhibit.json --synapseconfig $synapseconfig
-    """
-}
-
-process RENDER_HE {
-    label "process_medium"
-
-    publishDir "$params.outdir/$workflow.runName",
-        mode: 'move'     
-    
-    echo params.echo
-
-    input:
-        tuple val(synid), file(ome)
-        file synapseconfig from synapseconfig
-
-    output:
-        file 'minerva'
-
-    stub:
-    """
-    mkdir minerva
-    touch minerva/index.html
-    touch minerva/exhibit.json
-    """
-
-    script:
-    """
-    wget -O story.json $params.heStory
-    python3  /minerva-author/src/save_exhibit_pyramid.py $ome $story 'minerva'
-    cp /index.html minerva
-    wget -O fix_he_exhibit.py $params.heScript
-    python3 fix_he_exhibit.py minerva/exhibit.json
-    wget -O inject_description.py $params.minerva_description_script
-    python3 inject_description.py minerva/exhibit.json -synid$synid --synapseconfig $synapseconfig
-    """
-}
-
diff --git a/modules/render_pyramid.nf b/modules/render_pyramid.nf
index 7df6c49..f0514f2 100644
--- a/modules/render_pyramid.nf
+++ b/modules/render_pyramid.nf
@@ -1,4 +1,6 @@
 process render_pyramid {
+  tag {"$meta.id"}
+  label "process_medium"
   input:
       tuple val(meta), file(image), file (story)
   output:
@@ -15,7 +17,6 @@ process render_pyramid {
   script:
     """
     python3  /minerva-author/src/save_exhibit_pyramid.py $image $story 'minerva'
-    cp /index.html minerva
     """
     
 }
diff --git a/modules/synapse.nf b/modules/synapse.nf
deleted file mode 100644
index ca65ef4..0000000
--- a/modules/synapse.nf
+++ /dev/null
@@ -1,17 +0,0 @@
-process SYNAPSE_GET {
-  label "process_low"
-  echo params.echo
-  input:
-    val synid
-  output:
-    tuple val(synid), file('*')
-  stub:
-  """
-  touch "test.tif"
-  """
-  script:
-  """
-  echo "synapse -c $params.synapseconfig get $synid"
-  synapse -c $params.synapseconfig get $synid
-  """
-}
\ No newline at end of file
diff --git a/modules/synapse2.nf b/modules/synapse2.nf
deleted file mode 100644
index 2971f5a..0000000
--- a/modules/synapse2.nf
+++ /dev/null
@@ -1,312 +0,0 @@
-// Create channel for synapse config
-if (params.synapse_config) {
-    ch_synapse_config = file(params.synapse_config, checkIfExists: true)
-} else {
-    exit 1, 'Please provide a Synapse config file for download authentication!'
-}
-
-params.convert = true
-params.outdir = 'test-outputs'
-params.thumbnail_width = 512
-params.thumbnail_quality = 85
-params.remove_bg = true
-params.level = -1
-params.dimred = 'umap'
-heStory = 'https://gist.githubusercontent.com/adamjtaylor/3494d806563d71c34c3ab45d75794dde/raw/d72e922bc8be3298ebe8717ad2b95eef26e0837b/unscaled.story.json'
-
-
-
-workflow SYNAPSE {
-
-    take:
-    ids
-
-
-    main:
-
-    synapse_show (
-        ids,
-        ch_synapse_config
-    )
-
-    // Get metadata into channels
-    synapse_show
-        .out
-        .metadata
-        .map { it -> synapseShowToMap(it) }
-        .set { ch_samples_meta }
-
-    synapse_get (
-        ch_samples_meta,
-        ch_synapse_config
-    )
-        .set {synapse_out}
-
-    emit: synapse_out
-
-        
-}
-
-workflow CONVERT {
-    take: images
-    main:
-    images
-        .filter {
-            it[0].ome == false
-        }
-        .set {bioformats}
-
-    bioformats2ometiff( bioformats)
-
-    images
-      .filter {
-         it[0].ome == true
-      }    
-      .mix (bioformats2ometiff.out)
-      .set {converted}
-
-    emit: converted
-}
-
-workflow THUMBNAIL {
-  take:
-  converted
-  
-  main:
-  converted
-    .branch {
-        h_and_e: it[0].h_and_e == true
-        multiplex: it[0].h_and_e == false
-    }
-    .set { type }
-
-    make_miniature ( type.multiplex )
-    make_thumbnail ( type.h_and_e)
-
-    make_miniature
-        .out
-        .mix ( make_thumbnail.out )
-        .set { thumbnails }
-
-    emit: thumbnails
-
-}
-
-workflow MINERVA {
-  take:
-  converted
-  
-  main:
-
-  autominerva_story(converted)
-  render_pyramid(autominerva_story.out)
-}
-
-
-workflow {
-    SYNAPSE ( Channel.from('syn27056837','syn24829433') )
-    CONVERT ( SYNAPSE.out)
-    THUMBNAIL ( CONVERT.out )
-    MINERVA ( CONVERT.out )
-}
-
-
-def synapseShowToMap(synapse_file) {
-        def meta = [:]
-        def category = ''
-        synapse_file.eachLine { line ->
-            def entries = [null, null]
-            if (!line.startsWith(' ') && !line.trim().isEmpty()) {
-                category = line.tokenize(':')[0]
-            } else {
-                entries = line.trim().tokenize('=')
-            }
-            meta["${category}|${entries[0]}"] = entries[1]
-        }
-        meta.id = meta['properties|id']
-        meta.name = meta['properties|name']
-        meta.md5 = meta['File|md5']
-        meta.ome = meta['properties|name'] ==~ /.+\.ome\.tif{1,2}$/
-        meta.h_and_e =  meta['annotations|ImagingAssayType'] == "['H&E']"
-        return meta.findAll{ it.value != null }
-    }
-
-process synapse_show {
-    tag "$id"
-    label 'process_low'
-
-    conda "bioconda::synapseclient=2.6.0"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/synapseclient:2.6.0--pyh5e36f6f_0' :
-        'quay.io/biocontainers/synapseclient:2.6.0--pyh5e36f6f_0' }"
-
-    input:
-    val id
-    path config
-
-    output:
-    path "*.txt"       , emit: metadata
-
-    script:
-    def args  = task.ext.args  ?: ''
-    def args2 = task.ext.args2 ?: ''
-    """
-    synapse \\
-        -c $config \\
-        show \\
-        $args \\
-        $id \\
-        $args2 \\
-        > ${id}.metadata.txt
-    rm $config
-    """
-}
-
-process synapse_get {
-    tag "$meta.id"
-    label 'process_low'
-    label 'error_retry'
-
-    conda "bioconda::synapseclient=2.6.0"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/synapseclient:2.6.0--pyh5e36f6f_0' :
-        'quay.io/biocontainers/synapseclient:2.6.0--pyh5e36f6f_0' }"
-
-    input:
-    val meta
-    path config
-
-    output:
-    tuple val(meta), path('*'), emit: image
-
-    script:
-    def args = task.ext.args ?: ''
-    """
-    synapse \\
-        -c $config \\
-        get \\
-        $args \\
-        $meta.id
-    shopt -s nullglob
-    for f in *\\ *; do mv "\${f}" "\${f// /_}"; done
-    """
-}
-
-process bioformats2ometiff {
-  label "process_medium"
-  input:
-      tuple val(meta), file(image) 
-  output:
-      tuple val(meta), file("${image.simpleName}.ome.tiff")
-  stub:
-  """
-  touch raw_dir
-  touch "${image.simpleName}.ome.tiff"
-  """
-  script:
-  if ( meta.h_and_e){
-  """
-  bioformats2raw $image 'raw_dir' --series 0
-  raw2ometiff 'raw_dir' "${image.simpleName}.ome.tiff" --rgb
-  """
-  } else {
-  """
-  bioformats2raw $image 'raw_dir'
-  raw2ometiff 'raw_dir' "${image.simpleName}.ome.tiff"
-  """
-  }
-}
-
-process make_miniature {
-  label "process_medium"
-  input:
-      tuple val(meta), file(image) 
-  output:
-      tuple val(meta), file('data/miniature.jpg')
-  publishDir "$params.outdir/$workflow.runName",
-    saveAs: {filename -> "${meta.id}/$workflow.runName/thumbnail.jpg"}
-  stub:
-  """
-  mkdir data
-  touch data/miniature.jpg
-  """
-  script:
-    """
-    mkdir data
-    python3 /miniature/docker/paint_miniature.py \
-      $image 'miniature.jpg' \
-      --remove_bg $params.remove_bg \
-      --level $params.level \
-      --dimred $params.dimred
-    """
-}
-
-process make_thumbnail {
-  label "process_medium"
-  errorStrategy 'ignore'
-  input:
-      tuple val(meta), file(image) 
-  output:
-      tuple val(meta), file('miniature.jpg')
-  publishDir "$params.outdir/$workflow.runName",
-    saveAs: {filename -> "${meta.id}/$workflow.runName/thumbnail.jpg"}
-  stub:
-  """
-  touch miniature.jpg
-  """
-  script:
-  """
-  convert $image  \\
-    -thumbnail '${params.thumbnail_width}x${params.thumbnail_width}>' \\
-    -unsharp 0x.5 \\
-    -scene 1 \\
-    -quality $params.thumbnail_quality \\
-    miniature.jpg
-  """
-}
-
-
-process autominerva_story {
-  errorStrategy 'ignore'
-  input:
-      tuple val(meta), file(image) 
-  output:
-      tuple val(meta), file(image), file('story.json')
-  publishDir "$params.outdir/$workflow.runName",
-    saveAs: {filename -> "${meta.id}/$workflow.runName/story.json"}
-  stub: 
-  """
-  touch story.json
-  """
-  script:
-  if (meta.h_and_e) {
-    """
-    wget -O story.json $heStory
-    """
-  } else {
-    """
-    python3 /auto-minerva/story.py $image > 'story.json'
-    """
-  }
-}
-
-process render_pyramid {
-  input:
-      tuple val(meta), file(image), file (story)
-  output:
-      tuple val(meta), path('minerva')
-  publishDir "$params.outdir/$workflow.runName",
-    saveAs: {filename -> "${meta.id}/$workflow.runName/minerva"}
-  stub:
-  """
-  mkdir minerva
-  touch minerva/tile1.png
-  touch minerva/author.json
-  touch minerva/index.html
-  """
-  script:
-    """
-    python3  /minerva-author/src/save_exhibit_pyramid.py $image $story 'minerva'
-    cp /index.html minerva
-    """
-}
\ No newline at end of file
diff --git a/modules/thumbnails.nf b/modules/thumbnails.nf
deleted file mode 100644
index f924710..0000000
--- a/modules/thumbnails.nf
+++ /dev/null
@@ -1,55 +0,0 @@
-process MINIATURE {
-    label "process_high"
-    
-    publishDir "$params.outdir/$workflow.runName", 
-        saveAs: "thumbnail.png"
-    
-    echo params.echo
-
-    input:
-        tuple val(synid), file(ome)
-    
-    output:
-        file 'data/miniature.png'
-    
-    stub:
-    """
-    mkdir data
-    touch data/miniature.png
-    """
-    
-    script:
-    """
-    mkdir data
-    python3 /miniature/docker/paint_miniature.py $ome 'miniature.png' --remove_bg $remove_bg --level $params.level
-    """
-}
-
-
-process RESIZE {
-    label "process_high"
-    
-    publishDir "$params.outdir/$workflow.runName", 
-        saveAs: "thumbnail.png"
-    
-    echo params.echo
-
-    input:
-        tuple val(synid), file(ome)
-    
-    output:
-        file 'data/miniature.png'
-    
-    stub:
-    """
-    mkdir data
-    touch data/miniature.png
-    """
-    
-    script:
-    """
-    mkdir data
-    magick $ome -resize 512x512 data/miniature.png
-    """
-}
-
diff --git a/subworkflows/minerva.nf b/subworkflows/minerva.nf
index 4c377ee..3abc19c 100644
--- a/subworkflows/minerva.nf
+++ b/subworkflows/minerva.nf
@@ -6,11 +6,23 @@ workflow MINERVA {
   converted
   
   main:
+
+  // If H&E, used a fixed story from the assets dir
   converted
     .filter {
-            it[0].minerva == true
-        }
-    .set {for_minerva }
-  autominerva_story(for_minerva)
-  render_pyramid(autominerva_story.out)
+      it[0].minerva && it[0].he
+    }
+    .map { it -> [it[0], it[1], file( "$projectDir/assets/he_story.json", checkIfExists: true)] }
+    .set { he_story }
+
+  // If not H&E, run auto-minerva
+  converted
+    .filter {
+      it[0].minerva && it[0].he == false
+    } |
+    autominerva_story |
+  // Mix with the `he_story` channel and render the pyramid
+      mix( he_story ) |
+      render_pyramid
+  
 }
diff --git a/subworkflows/samplesheet_split.nf b/subworkflows/samplesheet_split.nf
index a08ac29..c6076b8 100644
--- a/subworkflows/samplesheet_split.nf
+++ b/subworkflows/samplesheet_split.nf
@@ -9,12 +9,7 @@ workflow SAMPLESHEET_SPLIT {
         .map { 
             row -> 
             def meta = [:]
-            if (row.id ) {
-                meta.id = row.id
-            } else {
-                meta.id = file(row.image).simpleName
-
-            }
+            meta.id = file(row.image).simpleName
             meta.ome = row.image ==~ /.+\.ome\.tif{1,2}$/
             meta.convert = row.convert.toBoolean()
             meta.he = row.he.toBoolean()
diff --git a/test.csv b/test.csv
deleted file mode 100644
index 78da384..0000000
--- a/test.csv
+++ /dev/null
@@ -1,2 +0,0 @@
-syn1234
-syn12345
\ No newline at end of file
diff --git a/test.nf b/test.nf
deleted file mode 100644
index 4f68c36..0000000
--- a/test.nf
+++ /dev/null
@@ -1,68 +0,0 @@
-#!/usr/bin/env nextflow
-
-// Enable dsl2
-nextflow.enable.dsl=2
-
-params.input_csv = './data/test.csv'
-params.input_path = false
-
-process SYNAPSE_GET {
-  label "process_low"
-  echo params.echo
-  input:
-    val synid
-  output:
-    tuple val(synid), file('*')
-  stub:
-  """
-  touch "test.tif"
-  """
-  script:
-  """
-  synapse -c ~/.synapseConfig get $synid
-  """
-}
-
-Channel
-    .fromPath(params.input_csv)
-    .splitText()
-    .set { input_csv }
-
-//input_csv.view()
-
-if (params.input_path != false) {
-  Channel
-    .fromPath(params.input_path)
-    .set { input_path }
-} else {
-    Channel.empty().set{input_path}
-}
-
-//input_path.view()
-
-Channel
-  .empty()
-  .mix(input_path)
-  .mix(input_csv)
-  .branch {
-    syn: it =~ /^syn\d+$/
-    other: true
-  }
-  .set { inputs }
-
-inputs.other
-  .map { it -> file(it) }
-  .map { it -> tuple(it.simpleName, it)}
-  .set {files}
-
-// files.view()
-
-workflow  {
-    SYNAPSE_GET(inputs.syn)
-    SYNAPSE_GET.out.view()
-    files
-      .mix(
-        SYNAPSE_GET.out
-      )
-      .view()
-}