initial commit

.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/build.yaml

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+name: Build
+
+on:
+  push:
+    branches: [ 'main' ]
+  workflow_dispatch:
+    inputs:
+      version:
+        description: |
+          The version of the project to build. Example: `1.0.3`.
+          
+          If not provided, a development build with a version name
+          based on the branch name will be built. Otherwise, a release
+          build with the provided version will be built.
+        required: false
+
+jobs:
+  build:
+    uses: openproblems-bio/actions/.github/workflows/build.yml@main
+    with:
+      version: ${{ github.event.inputs.version }}

.github/workflows/test.yaml

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+name: Test
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  build:
+    uses: openproblems-bio/actions/.github/workflows/test.yml@main

.gitignore

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+resources
+resources_test
+work
+.nextflow*
+target
+.vscode
+.DS_Store
+output
+trace-*
+.ipynb_checkpoints

.gitmodules

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+[submodule "common"]
+	path = common
+	url = https://github.com/openproblems-bio/common_resources.git

INSTRUCTIONS.md

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+# Instructions
+
+This is a guide on what to do after you have created a new task repository from the template. More in depth information about how to create a new task can be found in the [OpenProblems Documentation](https://openproblems.bio/documentation/create_task/).
+
+## Requirments
+
+A list of required software to start developing a new task can be found in the [OpenProblems Requirements](https://openproblems.bio/documentation/create_task/requirements).
+
+## First things first
+
+### `_viash.yaml`
+
+* Update the `name` field to the name of the task in snake_case the nane should start with `task_`.
+* Update the `description` field to a short description of the task.
+* Add a keyword to the `keywords` field that describes the task.
+* Update the `task_template` in the links/info field to the name of the task in snake_case.
+
+### `task_info.yaml`
+
+* Update the `src/api/task_info.yaml` file with the information you have provided in the task issue.
+* Update the `<task_name>` in the `readme` field to the name of the task.
+
+### `common` submodule
+
+If the submodule does not show any files, you will need to initialize the `common` submodule by running the following command:
+
+```bash
+git submodule update --init --recursive
+```
+
+To update the repository with the latest changes from in the submodule, you can run the following command:
+
+```bash
+git pull --recurse-submodules
+```
+
+## Resources
+
+The OpenProblems team has provided some test resources that can be used to test the task. These resources are stored in the `resources_test` folder. The `scripts/download_resources.sh` script can be used to download these resources.
+If these resources are not sufficient, you can add more resources to the `resources_test` folder. The `scripts/download_resources.sh` script can be updated to download these resources. When using new test resources let the OP team know so they can be added to the s3 bucket.
+
+```bash	
+scripts/download_resources.sh
+```
+
+## Next steps
+
+### API files ([docs](https://openproblems.bio/documentation/create_task/design_api))
+
+Update the API files in the `src/api` folder. These files define the input and output of the methods and metrics. 
+
+### Components ([docs](https://openproblems.bio/documentation/create_task/create_components))
+
+To create a component, you can run the respective script in the `script` directory. Before running the script make sure to update the variables `task_name`, `component_name` and `component_lang` and save the file. For additionale components ou will only need to update the `component_name` and `component_lang` variables.
+
+```bash
+scripts/add_a_control_method.sh
+```
+
+```bash
+scripts/add_a_method.sh
+```
+
+```bash
+scripts/add_a_metric.sh
+```
+
+For each type of component there already is a first component created that you can modify.
+
+1. Update the `.info` fields in the  `config.vsh.yaml`.
+2. Add any component specific arguments to the `config.vsh.yaml` file.
+3. Add any additional reqources that are required for the component.
+4. Update the docker engine image setup if additional packages are required.
+5. If you know the required memory and or CPU you can adjust the nextflow `.directive.labels` field. In addition if your component requires a GPU you can add the `gpu` label to the field.
+6. Update the `script.py` or `script.R` file with the code for the component.
+
+> [!NOTE]
+> You can remove the comments in the `config.vsh.yaml` file after you have updated the file.
+
+### Testing Components ([docs](https://openproblems.bio/documentation/create_component/run_tests))
+
+You can test the component by running the following command:
+
+```bash
+viash test /path/to/config.vsh.yaml
+```
+
+Y0u can also test all components by running the following command:
+
+```bash
+scripts/test_all_components.sh
+```
+
+It is possible to custumise the command in the above script by adding a `-q` argument to only perform the test on for example methods e.g. ` -q methods`.
+
+
+## Dataset processor ([docs](https://openproblems.bio/documentation/create_task/dataset_processor))
+
+The dataset processor is a script that removes all unnecesary info from the dataset for your task. This info is defined in the `api/file_common_dataset.yaml` file. From this filtered dataset several files are created that are used by the methods and metrics. Safeguarding data leaks and laking sure the structure of the data cannot be altered for a method or a metric.
+
+To create the dataprocessor there is no template available. You can follow the guideline in the documentation. Store the processor in the `src/process_dataset` folder.
+
+Be sure to update the `file_common_dataset.yaml` file with the correct information required for the methods/metrics.
+
+> [!IMPORTANT]
+> When using your own datasets please advise the openproblems team on how to add these datasets to the s3 bucket.
+> As the dataset processor should make use of the `common` datasets folder in the `resources` or `resources_test` directory.
+
+To create the resources  and test_resources for the task we will create a nextflow workflow that will process the datasets. This workflow will be created together with the openproblems team.
+
+## README
+
+To create the task `README` file preform following command:
+
+```bash
+scripts/create_readme.sh
+```
+
+## Benchmarking ([docs](https://openproblems.bio/documentation/create_task/create_workflow))
+
+When you are finished with creating your components and datset processor you can create a workflow to benchmark the components. This workflow will be created together with the openproblems team.

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.

README.md

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+# Task Template
+
+This repo is a template to create a new task for the OpenProblems v2. This repo contains several example files and components that can be used when updated with the task info.
+
+> [!WARNING] 
+> This README will be overwritten when performing the `create_task_readme` script.
+
+## Create a repository from this template
+
+> [!IMPORTANT] 
+> Before creating a new repository, make sure you are part of the openProblems task team. This will be done when you create an issue for the task and you got the go ahead to create the task.
+> For more information on how to create a new task, check out the [Create a new task](https://openproblems.bio/documentation/create_task/) documentation.
+
+The instructions below will guide you through creating a new repository from this template ([creating-a-repository-from-a-template](https://docs.github.com/en/repositories/creating-and-managing-repositories/creating-a-repository-from-a-template#creating-a-repository-from-a-template)).
+
+
+* Click the "Use this template" button on the top right of the repository.
+* Use the Owner dropdown menu to select the `openproblems-bio` account.
+* Type a name for your repository (task_...), and a description.
+* Set the repository visibility to public.
+* Click "Create repository from template".
+
+## Clone the repository
+
+To clone the repository with the submodule files, you can use the following command:
+
+```bash
+git clone --recursive [email protected]:openproblems-bio/task_spatial_simulators.git
+```
+
+If you already cloned the repository and forgot to use the `--recursive` flag, you can use the following command to update the submodules:
+
+```bash
+git submodule update --init --recursive
+```
+
+## What to do next
+
+Check out the [instructions](common/INSTRUCTIONS.md) for more information on how to update the example files and components. These instructions also contain information on how to build out the task and basic commands.
+
+For more information on the OpenProblems v2, check out the [Documentation](https://openproblems.bio/documentation/).

_viash.yaml

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+viash_version: 0.9.0-RC6
+
+name: task_template
+organization: openproblems-bio
+description: |
+  An OpenProblems benchmark task.
+license: MIT
+keywords: [single-cell, openproblems, benchmark]
+links:
+  issue_tracker: https://github.com/openproblems-bio/task_template/issues
+  repository: https://github.com/openproblems-bio/task_template
+  docker_registry: ghcr.io
+info:
+  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
+
+version: dev
+
+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" }

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/add_a_control_method.sh

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+#!/bin/bash
+
+task_name="task_template"
+component_name="my_control_method"
+component_lang="python" # change this to "r" if need be
+
+common/create_component/create_component \
+  --task $task_name \
+  --language "$component_lang" \
+  --name "$component_name" \
+  --api_file src/api/comp_control_method.yaml \
+  --output "src/control_methods/$component_name"

scripts/add_a_method.sh

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+#!/bin/bash
+
+task_name="task_template"
+component_name="my_method"
+component_lang="python" # change this to "r" if need be
+
+common/create_component/create_component \
+  --task $task_name \
+  --language "$component_lang" \
+  --name "$component_name" \
+  --api_file src/api/comp_method.yaml \
+  --output "src/methods/$component_name"

scripts/add_a_metric.sh

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+#!/bin/bash
+
+task_name="task_template"
+component_name="my_metric"
+component_lang="python" # change this to "r" if need be
+
+common/create_component/create_component \
+  --task $task_name \
+  --language "$component_lang" \
+  --name "$component_name" \
+  --api_file src/api/comp_metric.yaml \
+  --output "src/metrics/$component_name"

scripts/create_readme.sh

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+#!/bin/bash
+
+common/create_task_readme/create_task_readme \
+    --task_dir src \
+    --output README.md