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Merge branch '853-include-new-task-metadata-in-manifest' of github.com:fractal-analytics-platform/fractal-tasks-core into 853-include-new-task-metadata-in-manifest
2 parents 83d13e9 + ff3b44c commit 74a1481

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fractal_tasks_core/__FRACTAL_MANIFEST__.json

Lines changed: 36 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -5,6 +5,10 @@
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"name": "Convert Cellvoyager to OME-Zarr",
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"category": "Conversion",
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"modality": "HCS",
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"tags": [
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"Yokogawa",
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"Cellvoyager"
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],
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"executable_non_parallel": "tasks/cellvoyager_to_ome_zarr_init.py",
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"executable_parallel": "tasks/cellvoyager_to_ome_zarr_compute.py",
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"meta_non_parallel": {
@@ -269,6 +273,10 @@
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"name": "Convert Cellvoyager Multiplexing to OME-Zarr",
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"category": "Conversion",
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"modality": "HCS",
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"tags": [
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"Yokogawa",
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"Cellvoyager"
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],
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"executable_non_parallel": "tasks/cellvoyager_to_ome_zarr_init_multiplex.py",
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"executable_parallel": "tasks/cellvoyager_to_ome_zarr_compute.py",
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"meta_non_parallel": {
@@ -555,6 +563,11 @@
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"output_types": {
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"is_3D": false
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},
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"category": "Image Processing",
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"modality": "HCS",
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"tags": [
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"Preprocessing"
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],
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"executable_non_parallel": "tasks/copy_ome_zarr_hcs_plate.py",
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"executable_parallel": "tasks/projection.py",
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"meta_non_parallel": {
@@ -676,6 +689,10 @@
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"output_types": {
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"illumination_corrected": true
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},
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"category": "Image Processing",
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"tags": [
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"Preprocessing"
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],
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"executable_parallel": "tasks/illumination_correction.py",
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"meta_parallel": {
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"cpus_per_task": 1,
@@ -741,6 +758,11 @@
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{
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"name": "Cellpose Segmentation",
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"category": "Segmentation",
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"tags": [
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"Deep Learning",
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"Convolutional Neural Network",
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"Instance Segmentation"
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],
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"executable_parallel": "tasks/cellpose_segmentation.py",
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"meta_parallel": {
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"cpus_per_task": 4,
@@ -1036,6 +1058,10 @@
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{
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"name": "Calculate Registration (image-based)",
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"category": "Registration",
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"modality": "HCS",
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"tags": [
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"Multiplexing"
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],
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"executable_non_parallel": "tasks/image_based_registration_hcs_init.py",
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"executable_parallel": "tasks/calculate_registration_image_based.py",
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"meta_non_parallel": {
@@ -1168,6 +1194,10 @@
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{
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"name": "Find Registration Consensus",
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"category": "Registration",
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"modality": "HCS",
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"tags": [
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"Multiplexing"
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],
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"executable_non_parallel": "tasks/init_group_by_well_for_multiplexing.py",
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"executable_parallel": "tasks/find_registration_consensus.py",
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"meta_non_parallel": {
@@ -1271,6 +1301,10 @@
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"registered": true
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},
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"category": "Registration",
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"modality": "HCS",
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"tags": [
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"Multiplexing"
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],
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"executable_parallel": "tasks/apply_registration_to_image.py",
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"meta_parallel": {
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"cpus_per_task": 1,
@@ -1386,6 +1420,7 @@
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},
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{
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"name": "Napari Workflows Wrapper",
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"category": "Measurement",
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"executable_parallel": "tasks/napari_workflows_wrapper.py",
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"meta_parallel": {
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"cpus_per_task": 8,
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],
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"has_args_schemas": true,
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"args_schema_version": "pydantic_v2",
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"authors": "Name FIXME, Name FIXME, Name FIXME"
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"authors": "Fractal Core Team"
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}

fractal_tasks_core/dev/create_manifest.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -152,5 +152,5 @@ def create_manifest(
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if __name__ == "__main__":
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PACKAGE = "fractal_tasks_core"
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AUTHORS = "Name FIXME, Name FIXME, Name FIXME"
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AUTHORS = "Fractal Core Team"
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create_manifest(package=PACKAGE, authors=AUTHORS)

fractal_tasks_core/dev/task_list.py

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Original file line numberDiff line numberDiff line change
@@ -24,6 +24,7 @@
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meta={"cpus_per_task": 1, "mem": 4000},
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category="Conversion",
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modality="HCS",
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tags=["Yokogawa", "Cellvoyager"],
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),
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CompoundTask(
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name="Convert Cellvoyager Multiplexing to OME-Zarr",
@@ -33,6 +34,7 @@
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meta={"cpus_per_task": 1, "mem": 4000},
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category="Conversion",
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modality="HCS",
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tags=["Yokogawa", "Cellvoyager"],
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),
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CompoundTask(
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name="Project Image (HCS Plate)",
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output_types={"is_3D": False},
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meta_init={"cpus_per_task": 1, "mem": 4000},
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meta={"cpus_per_task": 1, "mem": 4000},
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category="Image Processing",
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modality="HCS",
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tags=["Preprocessing"],
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),
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ParallelTask(
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name="Illumination Correction",
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input_types=dict(illumination_corrected=False),
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executable="tasks/illumination_correction.py",
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output_types=dict(illumination_corrected=True),
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meta={"cpus_per_task": 1, "mem": 4000},
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category="Image Processing",
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tags=["Preprocessing"],
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),
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ParallelTask(
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name="Cellpose Segmentation",
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executable="tasks/cellpose_segmentation.py",
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meta={"cpus_per_task": 4, "mem": 16000, "needs_gpu": True},
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category="Segmentation",
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tags=[
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"Deep Learning",
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"Convolutional Neural Network",
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"Instance Segmentation",
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],
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),
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CompoundTask(
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name="Calculate Registration (image-based)",
@@ -63,6 +75,8 @@
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meta_init={"cpus_per_task": 1, "mem": 1000},
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meta={"cpus_per_task": 1, "mem": 8000},
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category="Registration",
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modality="HCS",
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tags=["Multiplexing"],
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),
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CompoundTask(
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name="Find Registration Consensus",
@@ -71,6 +85,8 @@
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meta_init={"cpus_per_task": 1, "mem": 1000},
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meta={"cpus_per_task": 1, "mem": 1000},
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category="Registration",
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modality="HCS",
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tags=["Multiplexing"],
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),
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ParallelTask(
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name="Apply Registration to Image",
@@ -79,6 +95,8 @@
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output_types=dict(registered=True),
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meta={"cpus_per_task": 1, "mem": 4000},
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category="Registration",
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modality="HCS",
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tags=["Multiplexing"],
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),
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NonParallelTask(
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name="Import OME-Zarr",
@@ -91,5 +109,6 @@
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"cpus_per_task": 8,
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"mem": 32000,
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},
112+
category="Measurement",
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),
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]

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