diff --git a/README.md b/README.md
index 973bdce..cafd684 100644
--- a/README.md
+++ b/README.md
@@ -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
@@ -155,23 +155,23 @@ Slot description:
-| 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. |
## 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.
@@ -179,11 +179,11 @@ Arguments:
-| 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. |
@@ -234,17 +234,17 @@ Slot description:
-| 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. |
@@ -259,11 +259,11 @@ Arguments:
-| 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. |
@@ -278,10 +278,10 @@ Arguments:
-| 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. |
@@ -296,11 +296,11 @@ Arguments:
-| 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. |
@@ -351,11 +351,11 @@ Slot description:
-| 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’. |
diff --git a/common b/common
index 95dcc63..b3db30d 160000
--- a/common
+++ b/common
@@ -1 +1 @@
-Subproject commit 95dcc63c124ab358ce7a7c48f916c51d55181172
+Subproject commit b3db30dc136f37c8b8b4cb866f1e5ca6c2304ee6
diff --git a/src/api/task_info.yaml b/src/api/task_info.yaml
index 7dc06b3..407f953 100644
--- a/src/api/task_info.yaml
+++ b/src/api/task_info.yaml
@@ -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 git@github.com: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