Merge pull request #13 from openproblems-bio/add_clustermap

Add clustermap

Author: LouisK92

.gitignore

@@ -20,4 +20,5 @@ singularity_container/
 /.nextflow*
 /work
 
-.DS_STORE
+*.DS_Store
+tmp

src/methods_transcript_assignment/clustermap_transcript_assignment/config.vsh.yaml

@@ -0,0 +1,154 @@
+__merge__: /src/api/comp_method_transcript_assignment.yaml
+
+name: clustermap_transcript_assignment
+label: "Clustermap Transcript Assignment"
+summary: "Assign transcripts to cells based on the ClusterMap method from He et al. 2021"
+description: "Clusters RNA transcripts using density peak clustering."
+links:
+  documentation: "https://github.com/wanglab-broad/ClusterMap"
+  repository: "https://github.com/wanglab-broad/ClusterMap"
+references:
+  doi: "10.1038/s41467-021-26044-x"
+
+arguments:
+  - name: --transcripts_key
+    type: string
+    description: The key of the transcripts within the points of the spatial data
+    default: transcripts
+  - name: --coordinate_system
+    type: string
+    description: The key of the pixel space coordinate system within the spatial data
+    default: global
+
+  - name: window_size
+    type: integer
+    required: false
+    description: "# small values to keep memory usage low, too small will lead to bad segmentations though"
+    direction: input 
+    default: 700
+
+  - name: use_dapi
+    type: boolean
+    required: false
+    description: "Whether to use the DAPI segmentation channel for clustermap"
+    direction: input 
+    default: True
+
+  - name: xy_radius
+    type: integer
+    required: false
+    description: "?"
+    direction: input 
+    default: 40
+
+  - name: z_radius
+    type: integer
+    required: false
+    description: "?"
+    direction: input 
+    default: 0
+
+  - name: fast_preprocess
+    type: boolean
+    required: false
+    description: "?"
+    direction: input 
+    default: False 
+
+  - name: gauss_blur
+    type: boolean
+    required: false
+    description: "Whether to apply gaussian blur to the DAPI image"
+    direction: input 
+    default: True
+    
+  - name: sigma
+    type: double
+    required: false
+    description: "Sigma parameter for for gaussian blur"
+    direction: input 
+    default: 1
+
+  - name: pct_filter
+    type: double
+    required: false
+    description: "Percent of transcripts to filter out. For example, pct_filter=0.1 will remove at 10% of transcripts"
+    direction: input 
+    default: 0.0
+
+  - name: LOF
+    type: boolean
+    required: false
+    description: "preprocess?"
+    direction: input 
+    default: False
+
+  - name: contamination
+    type: double
+    required: false
+    description: "?"
+    direction: input 
+    default: 0
+
+  - name: min_spot_per_cell
+    type: integer
+    required: false
+    description: "Minimum transcripts per cell"
+    direction: input 
+    default: 5
+
+  - name: add_dapi
+    type: boolean
+    required: false
+    description: "?"
+    direction: input 
+    default: True
+
+  - name: use_genedis
+    type: boolean
+    required: false
+    description: "?"
+    direction: input 
+    default: True
+
+  - name: dapi_grid_interval
+    type: integer
+    required: false
+    description: "?"
+    direction: input 
+    default: 5
+
+  - name: cell_num_threshold
+    type: double
+    required: false
+    description: "A threshold for deciding the number of cells. A larger value gives more cells"
+    direction: input 
+    default: 0.1
+
+resources:
+  - type: python_script
+    path: script.py
+
+engines:
+  - type: docker
+    image: openproblems/base_python:1.0.0
+    __merge__: 
+      - /src/base/setup_spatialdata_partial.yaml
+    setup:
+      - type: python
+        pypi: [anndata, PyYAML, imagecodecs, fastdist, h5py, imageio, natsort, networkx, opencv-python, pynndescent, pywavelets, scanpy, scikit-image, sinfo, stdlib-list, tifffile, tqdm, umap-learn, xlrd]
+      - type: docker
+        run: |
+          apt-get update && \
+          apt-get install -y libgl1-mesa-glx libglib2.0-0 && \
+          git clone https://github.com/wanglab-broad/ClusterMap.git && \
+          cd ClusterMap && \
+          pip install -e .
+      #  #github: [wanglab-broad/ClusterMap]
+  - type: native
+
+runners:
+  - type: executable
+  - type: nextflow
+    directives:
+      label: [ midtime, midcpu, highmem ]