diff --git a/CHANGELOG.md b/CHANGELOG.md index 794c5618f..e28ea5a75 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -34,6 +34,7 @@ * Update scPRINT to use latest stable version (PR #70) * Fix kbet dependencies to numpy<2 and scipy<=1.13 (PR #78). +* Fix `render_readme` crashing on `comp_process_integration.yaml`'s absolute `__merge__` paths. * Split Scanorama into two methods/scores - Split Scanorama into embedding (integrate) and count-correction (correct) modes, instead of running both together. diff --git a/README.md b/README.md index 7fab7a52a..e46ee430d 100644 --- a/README.md +++ b/README.md @@ -26,7 +26,7 @@ aim to remove batch effects scRNA-seq datasets \[@zappia2018exploring\]. These methods balance the removal of batch effects with the conservation of nuanced biological information in different ways. This abundance of tools has complicated batch integration method choice, leading to -several benchmarks on this topic \[@luecken2020benchmarking; +several benchmarks on this topic \[@luecken2022benchmarking; @tran2020benchmark; @chazarragil2021flexible; @mereu2020benchmarking\]. Yet, benchmarks use different metrics, method implementations and datasets. Here we build a living benchmarking task for batch integration @@ -46,15 +46,18 @@ extensive benchmark of single-cell data integration methods. ## Authors & contributors -| name | roles | -|:------------------|:-------------------| -| Michaela Mueller | maintainer, author | -| Malte Luecken | author | -| Daniel Strobl | author | -| Robrecht Cannoodt | contributor | -| Scott Gigante | contributor | -| Kai Waldrant | contributor | -| Nartin Kim | contributor | +| Name | Roles | Orcid | Github | +|:------------------|:-------------------|:--------------------|:-------------| +| Michaela Mueller | maintainer, author | 0000-0002-1401-1785 | mumichae | +| Malte Luecken | author | 0000-0001-7464-7921 | LuckyMD | +| Daniel Strobl | author | 0000-0002-5516-7057 | danielStrobl | +| Robrecht Cannoodt | author | 0000-0003-3641-729X | rcannood | +| Luke Zappia | author | 0000-0001-7744-8565 | lazappi | +| Scott Gigante | contributor | 0000-0002-4544-2764 | scottgigante | +| Kai Waldrant | contributor | 0009-0003-8555-1361 | KaiWaldrant | +| Martin Kim | contributor | 0009-0003-8555-1361 | martinkim0 | +| Sai Nirmayi Yasa | contributor | 0009-0003-6319-9803 | sainirmayi | +| Jeremie Kalfon | contributor | 0000-0002-2818-9728 | jkobject | ## API @@ -64,27 +67,27 @@ flowchart TB comp_process_dataset[/"Data processor"/] file_dataset("Dataset") file_solution("Solution") - comp_control_method[/"Control method"/] comp_method[/"Method"/] - comp_process_integration[/"Process integration"/] - comp_metric[/"Metric"/] + comp_control_method[/"Control method"/] file_integrated("Integration") + comp_process_integration[/"Process integration"/] file_integrated_processed("Processed integration output") + comp_metric[/"Metric"/] file_score("Score") file_common_dataset---comp_process_dataset comp_process_dataset-->file_dataset comp_process_dataset-->file_solution - file_dataset---comp_control_method file_dataset---comp_method + file_dataset---comp_control_method file_dataset---comp_process_integration file_solution---comp_control_method file_solution---comp_metric - comp_control_method-->file_integrated comp_method-->file_integrated - comp_process_integration-->file_integrated_processed - comp_metric-->file_score + comp_control_method-->file_integrated file_integrated---comp_process_integration + comp_process_integration-->file_integrated_processed file_integrated_processed---comp_metric + comp_metric-->file_score ``` ## File format: Common Dataset @@ -149,7 +152,7 @@ Arguments: | `--input` | `file` | A subset of the common dataset. | | `--output_dataset` | `file` | (*Output*) Unintegrated AnnData HDF5 file. | | `--output_solution` | `file` | (*Output*) Uncensored dataset containing the true labels. | -| `--hvgs` | `integer` | (*Optional*) NA. Default: `2000`. | +| `--hvgs` | `integer` | (*Optional*) Subset the count matrix to this number of HVGs. Default: `2000`. | @@ -249,22 +252,6 @@ Data structure: -## Component type: Control method - -A control method for the batch integration task. - -Arguments: - -
- -| Name | Type | Description | -|:-------------------|:-------|:-----------------------------------------------| -| `--input_dataset` | `file` | Unintegrated AnnData HDF5 file. | -| `--input_solution` | `file` | Uncensored dataset containing the true labels. | -| `--output` | `file` | (*Output*) An integrated AnnData dataset. | - -
- ## Component type: Method A method for the batch integration task. @@ -280,39 +267,19 @@ Arguments: -## Component type: Process integration - -Process output from an integration method to the format expected by -metrics - -Arguments: - -
- -| Name | Type | Description | -|:---|:---|:---| -| `--input_dataset` | `file` | Unintegrated AnnData HDF5 file. | -| `--input_integrated` | `file` | An integrated AnnData dataset. | -| `--expected_method_types` | `string` | NA. | -| `--expected_method_types` | `string` | NA. | -| `--expected_method_types` | `string` | NA. | -| `--output` | `file` | (*Output*) An integrated AnnData dataset with additional outputs. | - -
- -## Component type: Metric +## Component type: Control method -A metric for evaluating batch integration methods. +A control method for the batch integration task. Arguments:
-| Name | Type | Description | -|:---|:---|:---| -| `--input_integrated` | `file` | An integrated AnnData dataset with additional outputs. | +| Name | Type | Description | +|:-------------------|:-------|:-----------------------------------------------| +| `--input_dataset` | `file` | Unintegrated AnnData HDF5 file. | | `--input_solution` | `file` | Uncensored dataset containing the true labels. | -| `--output` | `file` | (*Output*) Metric score file. | +| `--output` | `file` | (*Output*) An integrated AnnData dataset. |
@@ -361,6 +328,24 @@ Data structure: +## Component type: Process integration + +Process output from an integration method to the format expected by +metrics + +Arguments: + +
+ +| Name | Type | Description | +|:---|:---|:---| +| `--input_dataset` | `file` | Unintegrated AnnData HDF5 file. | +| `--input_integrated` | `file` | An integrated AnnData dataset. | +| `--expected_method_types` | `string` | The expected output types of the batch integration method. | +| `--output` | `file` | (*Output*) An integrated AnnData dataset with additional outputs. | + +
+ ## File format: Processed integration output An integrated AnnData dataset with additional outputs. @@ -410,6 +395,22 @@ Data structure: +## Component type: Metric + +A metric for evaluating batch integration methods. + +Arguments: + +
+ +| Name | Type | Description | +|:---|:---|:---| +| `--input_integrated` | `file` | An integrated AnnData dataset with additional outputs. | +| `--input_solution` | `file` | Uncensored dataset containing the true labels. | +| `--output` | `file` | (*Output*) Metric score file. | + +
+ ## File format: Score Metric score file @@ -438,4 +439,3 @@ Data structure: | `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 67da19a36..deb906ef7 160000 --- a/common +++ b/common @@ -1 +1 @@ -Subproject commit 67da19a36ae56ea068804d15ccadec88a06da920 +Subproject commit deb906ef7abacf8809291631372c8aacadabeae9 diff --git a/scripts/create_readme.sh b/scripts/create_readme.sh index 0ed7aafe9..432aab468 100755 --- a/scripts/create_readme.sh +++ b/scripts/create_readme.sh @@ -2,4 +2,4 @@ set -e -common/scripts/create_task_readme --input src/api +common/scripts/create_task_readme diff --git a/src/api/comp_process_integration.yaml b/src/api/comp_process_integration.yaml index 944df29cf..e6162c012 100644 --- a/src/api/comp_process_integration.yaml +++ b/src/api/comp_process_integration.yaml @@ -14,12 +14,12 @@ argument_groups: - name: Inputs arguments: - name: "--input_dataset" - __merge__: /src/api/file_dataset.yaml + __merge__: file_dataset.yaml type: file direction: input required: true - name: "--input_integrated" - __merge__: /src/api/file_integrated.yaml + __merge__: file_integrated.yaml type: file direction: input required: true