add viash template

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: [bug]
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/config.yml

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+blank_issues_enabled: true

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: [enhancement]
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/PULL_REQUEST_TEMPLATE.md

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+## Describe your changes
+
+<!-- Describe your changes  -->
+
+## Checklist before requesting a review
+- [ ] I have performed a self-review of my code
+
+- Check the correct box. Does this PR contain:
+  - [ ] Breaking changes
+  - [ ] New functionality
+  - [ ] Major changes
+  - [ ] Minor changes
+  - [ ] Bug fixes
+
+- [ ] Proposed changes are described in the CHANGELOG.md
+
+- [ ] CI Tests succeed and look good!

.github/workflows/test.yaml

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+name: Test
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+jobs:
+  build:
+    uses: viash-io/viash-actions/.github/workflows/test.yaml@v6

.gitignore

@@ -10,3 +10,7 @@ temp/
 dependency.png
 envs/src/
 singularity_container/
+
+target
+.nextflow
+.resources_test

.gitmodules

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+[submodule "common"]
+	path = common
+	url = [email protected]:openproblems-bio/common_resources.git

CHANGELOG.md

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+# task_template x.y.z
+
+## BREAKING CHANGES
+
+<!-- * Restructured `src` directory (PR #3). -->
+
+## NEW FUNCTIONALITY
+
+* Added `control_methods/true_labels` component (PR #5).
+
+* Added `methods/logistic_regression` component (PR #5).
+
+* Added `metrics/accuracy` component (PR #5).
+
+## MAJOR CHANGES
+
+* Updated `api` files (PR #5).
+
+* Updated configs, components and CI to the latest Viash version (PR #8).
+
+## MINOR CHANGES
+
+* Updated `README.md` (PR #5).
+
+## BUGFIXES
+

LICENSE

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+MIT License
+
+Copyright (c) 2024 Open Problems in Single-Cell Analysis
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

_viash.yaml

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+viash_version: 0.9.0-RC7
+
+# Step 1: Change the name of the task.
+# example: task_name_of_this_task
+name: task_preprocessing_imagingbased_st
+organization: openproblems-bio
+version: dev
+
+license: MIT
+# Step 2: Add keywords to describe the task.
+keywords: [single-cell, openproblems, benchmark]
+# Step 3: Update the `task_template` to the name of the task from step 1.
+links:
+  issue_tracker: https://github.com/openproblems-bio/task_preprocessing_imagingbased_st/issues
+  repository: https://github.com/openproblems-bio/task_preprocessing_imagingbased_st
+  docker_registry: ghcr.io
+
+
+# Step 4: Update the label, summary and description.
+# A unique, human-readable, short label. Used for creating summary tables and visualisations.
+label: Template
+summary: A one sentence summary of purpose and methodology. Used for creating an overview tables.
+description: |
+  Provide a clear and concise description of your task, detailing the specific problem it aims
+  to solve. Outline the input data types, the expected output, and any assumptions or constraints.
+  Be sure to explain any terminology or concepts that are essential for understanding the task.
+
+  Explain the motivation behind your proposed task. Describe the biological or computational 
+  problem you aim to address and why it's important. Discuss the current state of research in
+  this area and any gaps or challenges that your task could help address. This section 
+  should convince readers of the significance and relevance of your task.
+
+# A list of references to relevant literature. Each reference should be a DOI or a bibtex entry
+references:
+  doi:
+    - 10.21203/rs.3.rs-4181617/v1
+  # bibtex:
+  #   - |
+  #     @article{doe_2021_template,
+  #       doi = {10.21203/rs.3.rs-4181617/v1},
+  #       url = {https://doi.org/10.21203/rs.3.rs-4181617/v1},
+  #       author = {Doe, John},
+  #       title = {A template for creating new tasks},
+  #       publisher = {Research Square},
+  #       year = {2021},
+  #     }
+
+info:
+  image: The name of the image file to use for the component on the website.
+  # Step 5: Replace the task_template to the name of the task.
+  test_resources:
+    - type: s3
+      path: s3://openproblems-data/resources_test/task_template/
+      dest: resources_test/task_template
+    - type: s3
+      path: s3://openproblems-data/resources_test/common/
+      dest: resources_test/common
+
+# Step 6: Update the authors of the task.
+authors: 
+  # Full name of the author, usually in the name of FirstName MiddleName LastName.
+  - name: John Doe
+    # Role of the author. Possible values:
+    # 
+    # * `"author"`: Authors who have made substantial contributions to the component.
+    # * `"maintainer"`: The maintainer of the component.
+    # * `"contributor"`: Authors who have made smaller contributions (such as code patches etc.).
+    roles: [ "author", "maintainer" ]
+    # Additional information on the author
+    info: 
+      github: johndoe
+      orcid: 0000-0000-0000-0000
+      email: [email protected]
+      twitter: johndoe
+      linkedin: johndoe
+
+# Step 7: Remove all of the comments of the steps you completed
+# Step 8: High five yourself!
+
+config_mods: |
+  .runners[.type == "nextflow"].config.labels := { lowmem : "memory = 20.Gb", midmem : "memory = 50.Gb", highmem : "memory = 100.Gb", lowcpu : "cpus = 5", midcpu : "cpus = 15", highcpu : "cpus = 30", lowtime : "time = 1.h", midtime : "time = 4.h", hightime : "time = 8.h", veryhightime : "time = 24.h" }
+
+repositories:
+  - name: openproblems-v2
+    type: github
+    repo: openproblems-bio/openproblems-v2
+    tag: main_build

main.nf

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+workflow {
+    print("This is a dummy placeholder for pipeline execution. Please use the corresponding nf files for running pipelines.")
+}

nextflow.config

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+process.container = 'nextflow/bash:latest'

scripts/.gitignore

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+add_a_method.sh
+add_a_control_method.sh
+add_a_metric.sh

src/api/comp_control_method.yaml

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+namespace: control_methods
+info:
+  type: control_method
+  type_info:
+    label: Control Method
+    summary: Quality control methods for verifying the pipeline.
+    description: |
+      This folder contains control components for the task. 
+      These components have the same interface as the regular methods
+      but also receive the solution object as input. It serves as a
+      starting point to test the relative accuracy of new methods in
+      the task, and also as a quality control for the metrics defined
+      in the task.
+arguments:
+  - name: --input_train
+    __merge__: file_train_h5ad.yaml
+    required: true
+    direction: input
+  - name: --input_test
+    __merge__: file_test_h5ad.yaml
+    required: true
+    direction: input
+  - name: "--input_solution"
+    __merge__: file_solution.yaml
+    direction: input
+    required: true
+  - name: --output
+    __merge__: file_prediction.yaml
+    required: true
+    direction: output
+test_resources:
+  - type: python_script
+    path: /common/component_tests/run_and_check_output.py
+  - type: python_script
+    path: /common/component_tests/check_config.py
+  - path: /resources_test/task_template/pancreas
+    dest: resources_test/task_template/pancreas

src/api/comp_data_processor.yaml

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+namespace: "data_processors"
+info:
+  type: data_processor
+  type_info:
+    label: Data processor
+    summary: A data processor.
+    description: |
+      A component for processing a Common Dataset into a task-specific dataset.
+arguments:
+  - name: "--input"
+    __merge__: file_common_dataset.yaml
+    direction: input
+    required: true
+  - name: "--output_train"
+    __merge__: file_train_h5ad.yaml
+    direction: output
+    required: true
+  - name: "--output_test"
+    __merge__: file_test_h5ad.yaml
+    direction: output
+    required: true
+  - name: "--output_solution"
+    __merge__: file_solution.yaml
+    direction: output
+    required: true
+test_resources:
+  - path: /resources_test/common/pancreas
+    dest: resources_test/common/pancreas
+  - type: python_script
+    path: /common/component_tests/run_and_check_output.py
+

src/api/comp_method.yaml

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+namespace: "methods"
+info:
+  type: method
+  type_info:
+    label: Method
+    summary: A method.
+    description: |
+      A method to predict the task effects.
+arguments:
+  - name: --input_train
+    __merge__: file_train_h5ad.yaml
+    required: true
+    direction: input
+  - name: "--input_test"
+    __merge__: file_test_h5ad.yaml
+    direction: input
+    required: true
+  - name: --output
+    __merge__: file_prediction.yaml
+    required: true
+    direction: output
+test_resources:
+  - type: python_script
+    path: /common/component_tests/run_and_check_output.py
+  - type: python_script
+    path: /common/component_tests/check_config.py
+  - path: /resources_test/task_template/pancreas
+    dest: resources_test/task_template/pancreas

src/api/comp_metric.yaml

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+namespace: "metrics"
+info:
+  type: metric
+  type_info:
+    label: Metric
+    summary: A task template metric.
+    description: |
+      A metric for evaluating method predictions.
+arguments:
+  - name: "--input_solution"
+    __merge__: file_solution.yaml
+    direction: input
+    required: true
+  - name: "--input_prediction"
+    __merge__: file_prediction.yaml
+    direction: input
+    required: true
+  - name: "--output"
+    __merge__: file_score.yaml
+    direction: output
+    required: true
+test_resources:
+  - type: python_script
+    path: /common/component_tests/run_and_check_output.py
+  - type: python_script
+    path: /common/component_tests/check_config.py
+  - path: /resources_test/task_template/pancreas
+    dest: resources_test/task_template/pancreas