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Remove readme field from task_info
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@KaiWaldrant
KaiWaldrant committed Jul 4, 2024
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88 changes: 44 additions & 44 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -60,7 +60,7 @@ Optionally, you can provide the `--query` argument to test only a subset
of components:

``` bash
viash ns test --parallel --query "component_name"
viash ns test --parallel --query 'component_name'
```

## Motivation
Expand Down Expand Up @@ -155,35 +155,35 @@ Slot description:

<div class="small">

| Slot | Type | Description |
|:-----------------------------|:----------|:-------------------------------------------------------------------------------|
| `layers["counts"]` | `integer` | Raw counts. |
| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. |
| `uns["dataset_name"]` | `string` | Nicely formatted name. |
| `uns["dataset_url"]` | `string` | (*Optional*) Link to the original source of the dataset. |
| `uns["dataset_reference"]` | `string` | (*Optional*) Bibtex reference of the paper in which the dataset was published. |
| `uns["dataset_summary"]` | `string` | Short description of the dataset. |
| `uns["dataset_description"]` | `string` | Long description of the dataset. |
| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. |
| Slot | Type | Description |
|:---|:---|:---|
| `layers["counts"]` | `integer` | Raw counts. |
| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. |
| `uns["dataset_name"]` | `string` | Nicely formatted name. |
| `uns["dataset_url"]` | `string` | (*Optional*) Link to the original source of the dataset. |
| `uns["dataset_reference"]` | `string` | (*Optional*) Bibtex reference of the paper in which the dataset was published. |
| `uns["dataset_summary"]` | `string` | Short description of the dataset. |
| `uns["dataset_description"]` | `string` | Long description of the dataset. |
| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. |

</div>

## Component type: Data processor

Path:
[`src/`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/)
[`src/process_dataset`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/process_dataset)

A denoising dataset processor.

Arguments:

<div class="small">

| Name | Type | Description |
|:-----------------|:-------|:------------------------------------------------------------------|
| `--input` | `file` | A subset of the common dataset. |
| Name | Type | Description |
|:---|:---|:---|
| `--input` | `file` | A subset of the common dataset. |
| `--output_train` | `file` | (*Output*) The subset of molecules used for the training dataset. |
| `--output_test` | `file` | (*Output*) The subset of molecules used for the test dataset. |
| `--output_test` | `file` | (*Output*) The subset of molecules used for the test dataset. |

</div>

Expand Down Expand Up @@ -234,17 +234,17 @@ Slot description:

<div class="small">

| Slot | Type | Description |
|:-----------------------------|:----------|:-------------------------------------------------------------------------------|
| `layers["counts"]` | `integer` | Raw counts. |
| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. |
| `uns["dataset_name"]` | `string` | Nicely formatted name. |
| `uns["dataset_url"]` | `string` | (*Optional*) Link to the original source of the dataset. |
| `uns["dataset_reference"]` | `string` | (*Optional*) Bibtex reference of the paper in which the dataset was published. |
| `uns["dataset_summary"]` | `string` | Short description of the dataset. |
| `uns["dataset_description"]` | `string` | Long description of the dataset. |
| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. |
| `uns["train_sum"]` | `integer` | The total number of counts in the training dataset. |
| Slot | Type | Description |
|:---|:---|:---|
| `layers["counts"]` | `integer` | Raw counts. |
| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. |
| `uns["dataset_name"]` | `string` | Nicely formatted name. |
| `uns["dataset_url"]` | `string` | (*Optional*) Link to the original source of the dataset. |
| `uns["dataset_reference"]` | `string` | (*Optional*) Bibtex reference of the paper in which the dataset was published. |
| `uns["dataset_summary"]` | `string` | Short description of the dataset. |
| `uns["dataset_description"]` | `string` | Long description of the dataset. |
| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. |
| `uns["train_sum"]` | `integer` | The total number of counts in the training dataset. |

</div>

Expand All @@ -259,11 +259,11 @@ Arguments:

<div class="small">

| Name | Type | Description |
|:----------------|:-------|:-------------------------------------------------------|
| Name | Type | Description |
|:---|:---|:---|
| `--input_train` | `file` | The subset of molecules used for the training dataset. |
| `--input_test` | `file` | The subset of molecules used for the test dataset. |
| `--output` | `file` | (*Output*) A denoised dataset as output by a method. |
| `--input_test` | `file` | The subset of molecules used for the test dataset. |
| `--output` | `file` | (*Output*) A denoised dataset as output by a method. |

</div>

Expand All @@ -278,10 +278,10 @@ Arguments:

<div class="small">

| Name | Type | Description |
|:----------------|:-------|:-------------------------------------------------------|
| Name | Type | Description |
|:---|:---|:---|
| `--input_train` | `file` | The subset of molecules used for the training dataset. |
| `--output` | `file` | (*Output*) A denoised dataset as output by a method. |
| `--output` | `file` | (*Output*) A denoised dataset as output by a method. |

</div>

Expand All @@ -296,11 +296,11 @@ Arguments:

<div class="small">

| Name | Type | Description |
|:---------------------|:-------|:---------------------------------------------------|
| `--input_test` | `file` | The subset of molecules used for the test dataset. |
| `--input_prediction` | `file` | A denoised dataset as output by a method. |
| `--output` | `file` | (*Output*) File indicating the score of a metric. |
| Name | Type | Description |
|:---|:---|:---|
| `--input_test` | `file` | The subset of molecules used for the test dataset. |
| `--input_prediction` | `file` | A denoised dataset as output by a method. |
| `--output` | `file` | (*Output*) File indicating the score of a metric. |

</div>

Expand Down Expand Up @@ -351,11 +351,11 @@ Slot description:

<div class="small">

| Slot | Type | Description |
|:-----------------------|:---------|:---------------------------------------------------------------------------------------------|
| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. |
| `uns["method_id"]` | `string` | A unique identifier for the method. |
| `uns["metric_ids"]` | `string` | One or more unique metric identifiers. |
| Slot | Type | Description |
|:---|:---|:---|
| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. |
| `uns["method_id"]` | `string` | A unique identifier for the method. |
| `uns["metric_ids"]` | `string` | One or more unique metric identifiers. |
| `uns["metric_values"]` | `double` | The metric values obtained for the given prediction. Must be of same length as ‘metric_ids’. |

</div>
Expand Down
2 changes: 1 addition & 1 deletion common
Submodule common updated from 95dcc6 to b3db30
46 changes: 0 additions & 46 deletions src/api/task_info.yaml
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Expand Up @@ -2,52 +2,6 @@ name: denoising
label: Denoising
summary: "Removing noise in sparse single-cell RNA-sequencing count data"
image: "thumbnail.svg"
readme: |
## Installation
You need to have Docker, Java, and Viash installed. Follow
[these instructions](https://openproblems.bio/documentation/fundamentals/requirements)
to install the required dependencies.
## Add a method
To add a method to the repository, follow the instructions in the `scripts/add_a_method.sh` script.
## Frequently used commands
To get started, you can run the following commands:
```bash
git clone [email protected]:openproblems-bio/task_denoising.git
cd task_denoising
# initialise submodule
scripts/init_submodule.sh
# download resources
scripts/download_resources.sh
```
To run the benchmark, you first need to build the components. Afterwards, you can run the benchmark:
```bash
viash ns build --parallel --setup cachedbuild
scripts/run_benchmark.sh
```
After adding a component, it is recommended to run the tests to ensure that the component is working correctly:
```bash
viash ns test --parallel
```
Optionally, you can provide the `--query` argument to test only a subset of components:
```bash
viash ns test --parallel --query "component_name"
```
motivation: |
Single-cell RNA-Seq protocols only detect a fraction of the mRNA molecules present
in each cell. As a result, the measurements (UMI counts) observed for each gene and each
Expand Down

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