diff --git a/.github/ISSUE_TEMPLATE/new_task.yml b/.github/ISSUE_TEMPLATE/new_task.yml index 1b275f4227..227357d5a6 100644 --- a/.github/ISSUE_TEMPLATE/new_task.yml +++ b/.github/ISSUE_TEMPLATE/new_task.yml @@ -4,7 +4,7 @@ labels: [task] body: - type: markdown attributes: - value: Thanks for choosing OpenProblems. Please check the [OpenProblems tasks](https://github.com/openproblems-bio/openproblems-v2/issues?q=label%3Atask+) to see whether a similar task has already been created. If you haven't already, please review the documentation on [how to create a new task](https://openproblems.bio/documentation/create_task/). + value: Thanks for choosing OpenProblems. Please check the [OpenProblems tasks](https://github.com/openproblems-bio/openproblems/issues?q=label%3Atask+) to see whether a similar task has already been created. If you haven't already, please review the documentation on [how to create a new task](https://openproblems.bio/documentation/create_task/). - type: textarea attributes: label: Task motivation @@ -16,7 +16,7 @@ body: - type: textarea attributes: label: Proposed ground-truth in datasets - description: Describe the datasets you plan to use for your task. OpenProblems offers a standard set of datasets (See [“Common datasets”](https://openproblems.bio/documentation/reference/openproblems-v2/src-datasets.html)) which you can peruse through. Explain how these datasets will provide the ground-truth for evaluating the methods implemented in your task. If possible, include references or links to the datasets to facilitate reproducibility. + description: Describe the datasets you plan to use for your task. OpenProblems offers a standard set of datasets (See [“Common datasets”](https://openproblems.bio/documentation/reference/openproblems/src-datasets.html)) which you can peruse through. Explain how these datasets will provide the ground-truth for evaluating the methods implemented in your task. If possible, include references or links to the datasets to facilitate reproducibility. - type: textarea attributes: label: Initial set of methods to implement diff --git a/.github/workflows/release-build.yml b/.github/workflows/release-build.yml index 7d89fac5cf..93b6f1eabf 100644 --- a/.github/workflows/release-build.yml +++ b/.github/workflows/release-build.yml @@ -16,7 +16,6 @@ jobs: outputs: component_matrix: ${{ steps.set_matrix.outputs.components }} - workflow_matrix: ${{ steps.set_matrix.outputs.workflows }} cache_key: ${{ steps.cache.outputs.cache_key }} steps: @@ -56,12 +55,6 @@ jobs: src: src format: json - - id: ns_list_workflows - uses: viash-io/viash-actions/ns-list@v6 - with: - src: workflows - format: json - - id: set_matrix run: | echo "components=$(jq -c '[ .[] | @@ -72,14 +65,6 @@ jobs: } ]' ${{ steps.ns_list_components.outputs.output_file }} )" >> $GITHUB_OUTPUT - echo "workflows=$(jq -c '[ .[] | - { - "name": (.functionality.namespace + "/" + .functionality.name), - "main_script": (.info.config | capture("^(?.*\/)").dir + "/" + .functionality.test_resources[].path), - "entry": .functionality.test_resources[].entrypoint - } - ]' ${{ steps.ns_list_workflows.outputs.output_file }} )" >> $GITHUB_OUTPUT - # phase 2 build: needs: list @@ -128,56 +113,6 @@ jobs: ###################################3 # phase 3 - integration_test: - needs: [ build, list ] - if: "${{ needs.list.outputs.workflow_matrix != '[]' }}" - - runs-on: ubuntu-latest - - strategy: - fail-fast: false - matrix: - component: ${{ fromJson(needs.list.outputs.workflow_matrix) }} - - steps: - # Remove unnecessary files to free up space. Otherwise, we get 'no space left on device.' - - uses: data-intuitive/reclaim-the-bytes@v2 - - - uses: actions/checkout@v4 - - - uses: viash-io/viash-actions/setup@v6 - - - uses: nf-core/setup-nextflow@v2.0.0 - - # build target dir - # use containers from release branch, hopefully these are available - - name: Build target dir - uses: viash-io/viash-actions/ns-build@v6 - with: - config_mod: ".functionality.version := '${{ github.event.inputs.version_tag }}'" - parallel: true - - # use cache - - name: Cache resources data - uses: actions/cache@v4 - timeout-minutes: 5 - with: - path: resources_test - key: ${{ needs.list.outputs.cache_key }} - - - name: Run integration test - timeout-minutes: 45 - run: | - # todo: replace with viash test command - export NXF_VER=22.04.5 - nextflow run . \ - -main-script "${{ matrix.component.main_script }}" \ - -entry ${{ matrix.component.entry }} \ - -profile docker,mount_temp,no_publish \ - -c workflows/utils/labels_ci.config - - ###################################3 - # phase 4 component_test: needs: [ build, list ] if: ${{ needs.list.outputs.component_matrix != '[]' && needs.list.outputs.component_matrix != '' }} @@ -208,4 +143,4 @@ jobs: --config_mod ".functionality.version := '${{ github.event.inputs.version_tag }}'" \ "${{ matrix.component.config }}" \ --cpus 2 \ - --memory "5gb" \ No newline at end of file + --memory "5gb" diff --git a/.gitignore b/.gitignore index c19f926ba4..4e328a4901 100644 --- a/.gitignore +++ b/.gitignore @@ -3,9 +3,11 @@ README_files/ *.DS_Store *__pycache__ *.h5ad +changelogs # IDE ignores /.idea/ +/.vscode/ # repo specific ignores output_bash diff --git a/.vscode/settings.json b/.vscode/settings.json index 7cb3263351..e662fc6472 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -5,12 +5,6 @@ "src/common/schemas/task_info.yaml": "src/**/api/task_info.yaml", "src/common/schemas/task_method.yaml": "src/tasks/**/methods/**/config.vsh.yaml", "src/common/schemas/task_control_method.yaml": "src/tasks/**/control_methods/**/config.vsh.yaml", - "src/common/schemas/task_metric.yaml": "src/tasks/**/metrics/**/config.vsh.yaml", - "/home/rcannood/.viash/releases/0.8.0/schema.json": [ - "*.vsh.yaml" - ], - "/home/rcannood/.viash/releases/0.8.6/schema.json": [ - "*.vsh.yaml" - ] + "src/common/schemas/task_metric.yaml": "src/tasks/**/metrics/**/config.vsh.yaml" } } \ No newline at end of file diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index a57b23cbb0..a141e7571d 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -1,20 +1,9 @@ # Contributing to OpenProblems - -- [Code of conduct](#code-of-conduct) -- [Requirements](#requirements) -- [Quick start](#quick-start) -- [Project structure](#project-structure) -- [Adding a Viash component](#adding-a-viash-component) -- [Running a component from CLI](#running-a-component-from-cli) -- [Building a component](#building-a-component) -- [Unit testing a component](#unit-testing-a-component) -- [More information](#more-information) -- [Branch Naming Conventions](#branch-naming-conventions) - [OpenProblems](https://openproblems.bio) is a community effort, and everyone is welcome to contribute. This project is hosted on -[github.com/openproblems-bio/openproblems-v2](https://github.com/openproblems-bio/openproblems-v2). +[github.com/openproblems-bio/openproblems](https://github.com/openproblems-bio/openproblems). + You can find a full in depth guide on how to contribute to this project on the [OpenProblems website](https://openproblems.bio/documentation/). @@ -33,607 +22,3 @@ welcoming, diverse, inclusive, and healthy community. Our full [Code of Conduct](CODE_OF_CONDUCT.md) is adapted from the [Contributor Covenant](https://www.contributor-covenant.org), version 2.1. - -## Requirements - -To use this repository, please install the following dependencies: - -- Bash -- Java (Java 11 or higher) -- Docker (Instructions [here](https://docs.docker.com/get-docker/)) -- Nextflow (Optional, though [very easy to - install](https://www.nextflow.io/index.html#GetStarted)) - -## Quick start - -The `src/` folder contains modular software components for running a -modality alignment benchmark. Running the full pipeline is quite easy. - -**Step 0, fetch Viash and Nextflow** - -``` bash -mkdir $HOME/bin -curl -fsSL get.viash.io | bash -s -- --bin $HOME/bin --tools false -curl -s https://get.nextflow.io | bash; mv nextflow $HOME/bin -``` - -Make sure that Viash and Nextflow are on the \$PATH by checking whether -the following commands work: - -``` bash -viash -v -nextflow -v -``` - - viash 0.8.0 (c) 2020 Data Intuitive - nextflow version 23.04.1.5866 - -**Step 1, download test resources:** by running the following command. - -``` bash -viash run src/common/sync_test_resources/config.vsh.yaml -``` - - Completed 256.0 KiB/7.2 MiB (302.6 KiB/s) with 6 file(s) remaining - Completed 512.0 KiB/7.2 MiB (595.8 KiB/s) with 6 file(s) remaining - Completed 768.0 KiB/7.2 MiB (880.3 KiB/s) with 6 file(s) remaining - Completed 1.0 MiB/7.2 MiB (1.1 MiB/s) with 6 file(s) remaining - Completed 1.2 MiB/7.2 MiB (1.3 MiB/s) with 6 file(s) remaining - ... - -**Step 2, build all the components:** in the `src/` folder as standalone -executables in the `target/` folder. Use the `-q 'xxx'` parameter to -build a subset of components in the repository. - -``` bash -viash ns build --query 'label_projection|common' --parallel --setup cachedbuild -``` - - In development mode with 'dev'. - Exporting process_dataset (label_projection) =docker=> target/docker/label_projection/process_dataset - Exporting accuracy (label_projection/metrics) =docker=> target/docker/label_projection/metrics/accuracy - Exporting random_labels (label_projection/control_methods) =docker=> target/docker/label_projection/control_methods/random_labels - [notice] Building container 'label_projection/control_methods_random_labels:dev' with Dockerfile - [notice] Building container 'common/data_processing_dataset_concatenate:dev' with Dockerfile - [notice] Building container 'label_projection/metrics_accuracy:dev' with Dockerfile - ... - -Viash will build a whole namespace (`ns`) into executables and Nextflow -pipelines into the `target/docker` and `target/nextflow` folders -respectively. By adding the `-q/--query` flag, you can filter which -components to build using a regex. By adding the `--parallel` flag, -these components are built in parallel (otherwise it will take a really -long time). The flag `--setup cachedbuild` will automatically start -building Docker containers for each of these methods. - -The command might take a while to run, since it is building a docker -container for each of the components. - -**Step 3, run the pipeline with nextflow.** To do so, run the bash -script located at -`src/tasks/label_projection/workflows/run_nextflow.sh`: - -``` bash -src/tasks/label_projection/workflows/run/run_test.sh -``` - - N E X T F L O W ~ version 22.04.5 - Launching `src/tasks/label_projection/workflows/run/main.nf` [pensive_turing] DSL2 - revision: 16b7b0c332 - executor > local (28) - [f6/f89435] process > run_wf:run_methods:true_labels:true_labels_process (pancreas.true_labels) [100%] 1 of 1 ✔ - [ed/d674a2] process > run_wf:run_methods:majority_vote:majority_vote_process (pancreas.majority_vote) [100%] 1 of 1 ✔ - [15/f0a427] process > run_wf:run_methods:random_labels:random_labels_process (pancreas.random_labels) [100%] 1 of 1 ✔ - [02/969d05] process > run_wf:run_methods:knn:knn_process (pancreas.knn) [100%] 1 of 1 ✔ - [90/5fdf9a] process > run_wf:run_methods:mlp:mlp_process (pancreas.mlp) [100%] 1 of 1 ✔ - [c7/dee2e5] process > run_wf:run_methods:logistic_regression:logistic_regression_process (pancreas.logistic_regression) [100%] 1 of 1 ✔ - [83/3ba0c9] process > run_wf:run_methods:scanvi:scanvi_process (pancreas.scanvi) [100%] 1 of 1 ✔ - [e3/2c298e] process > run_wf:run_methods:seurat_transferdata:seurat_transferdata_process (pancreas.seurat_transferdata) [100%] 1 of 1 ✔ - [d6/7212ab] process > run_wf:run_methods:xgboost:xgboost_process (pancreas.xgboost) [100%] 1 of 1 ✔ - [b6/7dc1a7] process > run_wf:run_metrics:accuracy:accuracy_process (pancreas.scanvi) [100%] 9 of 9 ✔ - [be/7d4da4] process > run_wf:run_metrics:f1:f1_process (pancreas.scanvi) [100%] 9 of 9 ✔ - [89/dcd77a] process > run_wf:aggregate_results:extract_scores:extract_scores_process (combined) [100%] 1 of 1 ✔ - -## Project structure - -High level overview: . ├── bin Helper scripts for building the project -and developing a new component. ├── resources_test Datasets for testing -components. If you don’t have this folder, run **Step 1** above. ├── src -Source files for each component in the pipeline. │ ├── common Common -processing components. │ ├── datasets Components and pipelines for -building the ‘Common datasets’ │ ├── label_projection Source files -related to the ‘Label projection’ task. │ └── … Other tasks. └── target -Executables generated by viash based on the components listed under -`src/`. ├── docker Bash executables which can be used from a terminal. -└── nextflow Nextflow modules which can be used as a standalone pipeline -or as part of a bigger pipeline. - -Detailed overview of a task folder (e.g. `src/tasks/label_projection`): - - src/tasks/label_projection/ - ├── api Specs for the components in this task. - ├── control_methods Control methods which serve as quality control checks for the benchmark. - ├── docs Task documentation - ├── methods Label projection method components. - ├── metrics Label projection metric components. - ├── resources_scripts The scripts needed to run the benchmark. - ├── resources_test_scripts The scripts needed to generate the test resources (which are needed for unit testing). - ├── process_dataset A component that masks a common dataset for use in the benchmark - └── workflows The benchmarking workflow. - -Detailed overview of the `src/datasets` folder: - - src/datasets/ - ├── api Specs for the data loaders and normalisation methods. - ├── loaders Components for ingesting datasets from a source. - ├── normalization Normalization method components. - ├── processors Other preprocessing components (e.g. HVG and PCA). - ├── resource_scripts The scripts needed to generate the common datasets. - ├── resource_test_scripts The scripts needed to generate the test resources (which are needed for unit testing). - └── workflows The workflow which generates the common datasets. - -## Adding a Viash component - -[Viash](https://viash.io) allows you to create pipelines in Bash or -Nextflow by wrapping Python, R, or Bash scripts into reusable -components. - -You can start creating a new component by [creating a Viash -component](https://viash.io/guide/component/creation/docker.html). - -For example, to create a new Python-based method named `foo`, create a -Viash config at -`src/tasks/label_projection/methods/foo/config.vsh.yaml`: - -``` yaml -__merge__: ../../api/comp_method.yaml -functionality: - name: "foo" - namespace: "label_projection/methods" - # A multiline description of your method. - description: "Todo: fill in" - info: - type: method - - # a short label of your method - label: Foo - - # A multiline description of your method. - description: "Todo: fill in" - - # A short summary of the method description. - summary: "Todo: fill in" - - # Add the bibtex reference to the "src/common/library.bib" if it is not already there. - reference: "cover1967nearest" - - repository_url: "https://github.com/openproblems-bio/openproblems-v2" - documentation_url: "https://openproblems.bio/documentation/" - preferred_normalization: log_cp10k - resources: - - type: python_script - path: script.py -platforms: - - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 - setup: - - type: python - packages: [scikit-learn] - - type: nextflow - directives: - label: [midtime, midmem, lowcpu] -``` - -And create a script at -`src/tasks/label_projection/methods/foo/script.py`: - -``` python -import anndata as ad -import numpy as np - -## VIASH START -# This code-block will automatically be replaced by Viash at runtime. -par = { - 'input_train': 'resources_test/label_projection/pancreas/train.h5ad', - 'input_test': 'resources_test/label_projection/pancreas/test.h5ad', - 'output': 'output.h5ad' -} -meta = { - 'functionality_name': 'foo' -} -## VIASH END - -print("Load data", flush=True) -input_train = ad.read_h5ad(par['input_train']) -input_test = ad.read_h5ad(par['input_test']) - -print("Create predictions", flush=True) -input_test.obs["label_pred"] = "foo" - -print("Add method name to uns", flush=True) -input_test.uns["method_id"] = meta["functionality_name"] - -print("Write output to file", flush=True) -input_test.write_h5ad(par["output"], compression="gzip") -``` - -## Running a component from CLI - -You can view the interface of the executable by running the executable -with the `-h` or `--help` parameter. - -``` bash -viash run src/tasks/label_projection/methods/foo/config.vsh.yaml -- --help -``` - - foo dev - - Todo: fill in - - Arguments: - --input_train - type: file, required parameter, file must exist - example: resources_test/label_projection/pancreas/train.h5ad - - --input_test - type: file, required parameter, file must exist - example: resources_test/label_projection/pancreas/test.h5ad - - --output - type: file, required parameter, output, file must exist - example: resources_test/label_projection/pancreas/prediction.h5ad - -Before running a new component, youy will need to create the docker -container: - -``` bash -viash run src/tasks/label_projection/methods/foo/config.vsh.yaml -- ---setup cachedbuild -``` - - [notice] Building container 'ghcr.io/openproblems-bio/label_projection/methods/foo:dev' with Dockerfile - -You can **run the component** as follows: - -``` bash -viash run src/tasks/label_projection/methods/foo/config.vsh.yaml -- \ - --input_train resources_test/label_projection/pancreas/train.h5ad \ - --input_test resources_test/label_projection/pancreas/test.h5ad \ - --output resources_test/label_projection/pancreas/prediction.h5ad -``` - - Load data - Create predictions - Add method name to uns - Write output to file - -## Building a component - -`viash` has several helper functions to help you quickly develop a -component. - -With **`viash build`**, you can turn the component into a standalone -executable. This standalone executable you can give to somebody else, -and they will be able to run it, provided that they have Bash and Docker -installed. - -``` bash -viash build src/tasks/label_projection/methods/foo/config.vsh.yaml \ - -o target/docker/label_projection/methods/foo -``` - -> [!NOTE] -> -> The `viash ns build` component does a much better job of setting up a -> collection of components. - -You can now view the same interface of the executable by running the -executable with the `-h` parameter. - -``` bash -target/docker/label_projection/methods/foo/foo -h -``` - - foo dev - - Todo: fill in - - Arguments: - --input_train - type: file, required parameter, file must exist - example: resources_test/label_projection/pancreas/train.h5ad - - --input_test - type: file, required parameter, file must exist - example: resources_test/label_projection/pancreas/test.h5ad - - --output - type: file, required parameter, output, file must exist - example: resources_test/label_projection/pancreas/prediction.h5ad - -Or **run the component** as follows: - -``` bash -target/docker/label_projection/methods/foo/foo \ - --input_train resources_test/label_projection/pancreas/train.h5ad \ - --input_test resources_test/label_projection/pancreas/test.h5ad \ - --output resources_test/label_projection/pancreas/prediction.h5ad -``` - - Load data - Create predictions - Add method name to uns - Write output to file - -## Unit testing a component - -The [method API -specifications](src/tasks/label_projection/api/comp_method.yaml) comes -with a generic unit test for free. This means you can unit test your -component using the **`viash test`** command. - -``` bash -viash test src/tasks/label_projection/methods/foo/config.vsh.yaml -``` - - Running tests in temporary directory: '/tmp/viash_test_foo11070556749764805852' - ==================================================================== - +/tmp/viash_test_foo11070556749764805852/build_executable/foo ---verbosity 6 ---setup cachedbuild - [notice] Building container 'ghcr.io/openproblems-bio/label_projection/methods/foo:test' with Dockerfile - [info] Running 'docker build -t ghcr.io/openproblems-bio/label_projection/methods/foo:test /tmp/viash_test_foo11070556749764805852/build_executable -f /tmp/viash_test_foo11070556749764805852/build_executable/tmp/dockerbuild-foo-VMKj2u/Dockerfile' - #0 building with "default" instance using docker driver - - #1 [internal] load build definition from Dockerfile - #1 transferring dockerfile: 658B done - #1 DONE 0.1s - - #2 [internal] load .dockerignore - #2 transferring context: 2B done - #2 DONE 0.1s - - #3 [internal] load metadata for ghcr.io/openproblems-bio/base_python:1.0.2 - #3 DONE 0.3s - - #4 [1/2] FROM ghcr.io/openproblems-bio/base_python:1.0.2@sha256:65a577a3de37665b7a65548cb33c9153b6881742345593d33fe02919c8d66a20 - #4 DONE 0.0s - - #5 [2/2] RUN pip install --upgrade pip && pip install --upgrade --no-cache-dir "scikit-learn" - #5 CACHED - - #6 exporting to image - #6 exporting layers done - #6 writing image sha256:b5c134ce2ab91a0e616d7362f6bd168e6494c4a1bd7c643d62d7ad65d8678c5b done - #6 naming to ghcr.io/openproblems-bio/label_projection/methods/foo:test 0.0s done - #6 DONE 0.0s - ==================================================================== - +/tmp/viash_test_foo11070556749764805852/test_check_method_config/test_executable - Load config data - Check general fields - Check info fields - Check platform fields - All checks succeeded! - ==================================================================== - +/tmp/viash_test_foo11070556749764805852/test_run_and_check_adata/test_executable - >> Running test 'run' - >> Checking whether input files exist - >> Running script as test - Load data - Create predictions - Add method name to uns - Write output to file - >> Checking whether output file exists - >> Reading h5ad files and checking formats - Reading and checking input_train - AnnData object with n_obs × n_vars = 326 × 500 - obs: 'label', 'batch' - var: 'hvg', 'hvg_score' - uns: 'dataset_id', 'normalization_id' - obsm: 'X_pca' - layers: 'counts', 'normalized' - Reading and checking input_test - AnnData object with n_obs × n_vars = 174 × 500 - obs: 'batch' - var: 'hvg', 'hvg_score' - uns: 'dataset_id', 'normalization_id' - obsm: 'X_pca' - layers: 'counts', 'normalized' - Reading and checking output - AnnData object with n_obs × n_vars = 174 × 500 - obs: 'batch', 'label_pred' - var: 'hvg', 'hvg_score' - uns: 'dataset_id', 'method_id', 'normalization_id' - obsm: 'X_pca' - layers: 'counts', 'normalized' - All checks succeeded! - ==================================================================== - SUCCESS! All 2 out of 2 test scripts succeeded! - Cleaning up temporary directory - -Let’s introduce a bug in the script and try running the test again. For -instance: - -``` python -import anndata as ad -import numpy as np - -## VIASH START -# This code-block will automatically be replaced by Viash at runtime. -par = { - 'input_train': 'resources_test/label_projection/pancreas/train.h5ad', - 'input_test': 'resources_test/label_projection/pancreas/test.h5ad', - 'output': 'output.h5ad' -} -meta = { - 'functionality_name': 'foo' -} -## VIASH END - -print("Load data", flush=True) -input_train = ad.read_h5ad(par['input_train']) -input_test = ad.read_h5ad(par['input_test']) - -print("Not creating any predictions!!!", flush=True) -# input_test.obs["label_pred"] = "foo" - -print("Not adding method name to uns!!!", flush=True) -# input_test.uns["method_id"] = meta["functionality_name"] - -print("Write output to file", flush=True) -input_test.write_h5ad(par["output"], compression="gzip") -``` - -If we now run the test, we should get an error since we didn’t create -all of the required output slots. - -``` bash -viash test src/tasks/label_projection/methods/foo/config.vsh.yaml -``` - - Running tests in temporary directory: '/tmp/viash_test_foo11839237358029204600' - ==================================================================== - +/tmp/viash_test_foo11839237358029204600/build_executable/foo ---verbosity 6 ---setup cachedbuild - [notice] Building container 'ghcr.io/openproblems-bio/label_projection/methods/foo:test' with Dockerfile - [info] Running 'docker build -t ghcr.io/openproblems-bio/label_projection/methods/foo:test /tmp/viash_test_foo11839237358029204600/build_executable -f /tmp/viash_test_foo11839237358029204600/build_executable/tmp/dockerbuild-foo-gPvc8b/Dockerfile' - #0 building with "default" instance using docker driver - - #1 [internal] load build definition from Dockerfile - #1 transferring dockerfile: 658B done - #1 DONE 0.1s - - #2 [internal] load .dockerignore - #2 transferring context: 2B done - #2 DONE 0.1s - - #3 [internal] load metadata for ghcr.io/openproblems-bio/base_python:1.0.2 - #3 DONE 0.3s - - #4 [1/2] FROM ghcr.io/openproblems-bio/base_python:1.0.2@sha256:65a577a3de37665b7a65548cb33c9153b6881742345593d33fe02919c8d66a20 - #4 DONE 0.0s - - #5 [2/2] RUN pip install --upgrade pip && pip install --upgrade --no-cache-dir "scikit-learn" - #5 CACHED - - #6 exporting to image - #6 exporting layers done - #6 writing image sha256:939f5846475192d821898f663f15872432e7a2c9033b38ac9b9522155270daf4 done - #6 naming to ghcr.io/openproblems-bio/label_projection/methods/foo:test 0.0s done - #6 DONE 0.0s - ==================================================================== - +/tmp/viash_test_foo11839237358029204600/test_check_method_config/test_executable - Load config data - Check general fields - Check info fields - Check platform fields - All checks succeeded! - ==================================================================== - +/tmp/viash_test_foo11839237358029204600/test_run_and_check_adata/test_executable - >> Running test 'run' - >> Checking whether input files exist - >> Running script as test - Load data - Not creating any predictions!!! - Not adding method name to uns!!! - Write output to file - >> Checking whether output file exists - >> Reading h5ad files and checking formats - Reading and checking input_train - AnnData object with n_obs × n_vars = 326 × 500 - obs: 'label', 'batch' - var: 'hvg', 'hvg_score' - uns: 'dataset_id', 'normalization_id' - obsm: 'X_pca' - layers: 'counts', 'normalized' - Reading and checking input_test - AnnData object with n_obs × n_vars = 174 × 500 - obs: 'batch' - var: 'hvg', 'hvg_score' - uns: 'dataset_id', 'normalization_id' - obsm: 'X_pca' - layers: 'counts', 'normalized' - Reading and checking output - AnnData object with n_obs × n_vars = 174 × 500 - Traceback (most recent call last): - obs: 'batch' - var: 'hvg', 'hvg_score' - File "/viash_automount/tmp/viash_test_foo11839237358029204600/test_run_and_check_adata/tmp//viash-run-foo-22aQh6.py", line 138, in - uns: 'dataset_id', 'normalization_id' - run_and_check(argset_args, cmd) - obsm: 'X_pca' - File "/viash_automount/tmp/viash_test_foo11839237358029204600/test_run_and_check_adata/tmp//viash-run-foo-22aQh6.py", line 81, in run_and_check - layers: 'counts', 'normalized' - check_slots(adata, arg) - File "/viash_automount/tmp/viash_test_foo11839237358029204600/test_run_and_check_adata/tmp//viash-run-foo-22aQh6.py", line 48, in check_slots - assert slot_item["name"] in struc_x,\ - AssertionError: File 'output.h5ad' is missing slot .obs['label_pred'] - ==================================================================== - ERROR! Only 1 out of 2 test scripts succeeded! - Unexpected error occurred! If you think this is a bug, please post - create an issue at https://github.com/viash-io/viash/issues containing - a reproducible example and the stack trace below. - - viash - 0.8.0 - Stacktrace: - java.lang.RuntimeException: Only 1 out of 2 test scripts succeeded! - at io.viash.ViashTest$.apply(ViashTest.scala:134) - at io.viash.Main$.mainCLI(Main.scala:253) - at io.viash.Main$.mainCLIOrVersioned(Main.scala:123) - at io.viash.Main$.main(Main.scala:58) - at io.viash.Main.main(Main.scala) - -## More information - -The [Viash reference docs](https://viash.io/reference/config/) page -provides information on all of the available fields in a Viash config, -and the [Guide](https://viash.io/guide/) will help you get started with -creating components from scratch. - - - -## Branch Naming Conventions - -### Category - -A git branch should start with a category. Pick one of these: feature, -bugfix, hotfix, or test. - -- `feature` is for adding, refactoring or removing a feature -- `bugfix` is for fixing a bug -- `hotfix` is for changing code with a temporary solution and/or without - following the usual process (usually because of an emergency) -- `test` is for experimenting outside of an issue/ticket -- `doc` is for adding, changing or removing documentation - -### Reference - -After the category, there should be a “`/`” followed by the reference of -the issue/ticket/task you are working on. If there’s no reference, just -add no-ref. With task it is meant as benchmarking task -e.g. batch_integration - -### Description - -After the reference, there should be another “`/`” followed by a -description which sums up the purpose of this specific branch. This -description should be short and “kebab-cased”. - -By default, you can use the title of the issue/ticket you are working -on. Just replace any special character by “`-`”. - -### To sum up, follow this pattern when branching: - -``` bash -git branch -``` - -### Examples - -- You need to add, refactor or remove a feature: - `git branch feature/issue-42/create-new-button-component` -- You need to fix a bug: - `git branch bugfix/issue-342/button-overlap-form-on-mobile` -- You need to fix a bug really fast (possibly with a temporary - solution): `git branch hotfix/no-ref/registration-form-not-working` -- You need to experiment outside of an issue/ticket: - `git branch test/no-ref/refactor-components-with-atomic-design` - -### References - -- [a-simplified-convention-for-naming-branches-and-commits-in-git](https://dev.to/varbsan/a-simplified-convention-for-naming-branches-and-commits-in-git-il4) diff --git a/CONTRIBUTING.qmd b/CONTRIBUTING.qmd deleted file mode 100644 index 6b6e33ae07..0000000000 --- a/CONTRIBUTING.qmd +++ /dev/null @@ -1,401 +0,0 @@ ---- -title: Contributing to OpenProblems -format: gfm -toc: true -toc-depth: 2 -engine: knitr ---- - -[OpenProblems](https://openproblems.bio) is a community effort, and everyone is welcome to contribute. This project is hosted on [github.com/openproblems-bio/openproblems-v2](https://github.com/openproblems-bio/openproblems-v2). You can find a full in depth guide on how to contribute to this project on the [OpenProblems website](https://openproblems.bio/documentation/). - -## Code of conduct {#code-of-conduct} - -We as members, contributors, and leaders pledge to make participation in our community a harassment-free experience for everyone, regardless of age, body size, visible or invisible disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, or sexual identity and orientation. - -We pledge to act and interact in ways that contribute to an open, welcoming, diverse, inclusive, and healthy community. - -Our full [Code of Conduct](CODE_OF_CONDUCT.md) is adapted from the [Contributor Covenant](https://www.contributor-covenant.org), version 2.1. - - -## Requirements - -To use this repository, please install the following dependencies: - -* Bash -* Java (Java 11 or higher) -* Docker (Instructions [here](https://docs.docker.com/get-docker/)) -* Nextflow (Optional, though [very easy to install](https://www.nextflow.io/index.html#GetStarted)) - -## Quick start - -The `src/` folder contains modular software components for running a modality alignment benchmark. Running the full pipeline is quite easy. - -**Step 0, fetch Viash and Nextflow** - -```bash -mkdir $HOME/bin -curl -fsSL get.viash.io | bash -s -- --bin $HOME/bin --tools false -curl -s https://get.nextflow.io | bash; mv nextflow $HOME/bin -``` - -Make sure that Viash and Nextflow are on the $PATH by checking whether the following commands work: - -```{bash} -viash -v -nextflow -v -``` - -**Step 1, download test resources:** by running the following command. - -```bash -viash run src/common/sync_test_resources/config.vsh.yaml -``` - - Completed 256.0 KiB/7.2 MiB (302.6 KiB/s) with 6 file(s) remaining - Completed 512.0 KiB/7.2 MiB (595.8 KiB/s) with 6 file(s) remaining - Completed 768.0 KiB/7.2 MiB (880.3 KiB/s) with 6 file(s) remaining - Completed 1.0 MiB/7.2 MiB (1.1 MiB/s) with 6 file(s) remaining - Completed 1.2 MiB/7.2 MiB (1.3 MiB/s) with 6 file(s) remaining - ... - -**Step 2, build all the components:** in the `src/` folder as standalone executables in the `target/` folder. Use the `-q 'xxx'` parameter to build a subset of components in the repository. - -```bash -viash ns build --query 'label_projection|common' --parallel --setup cachedbuild -``` - - In development mode with 'dev'. - Exporting process_dataset (label_projection) =docker=> target/docker/label_projection/process_dataset - Exporting accuracy (label_projection/metrics) =docker=> target/docker/label_projection/metrics/accuracy - Exporting random_labels (label_projection/control_methods) =docker=> target/docker/label_projection/control_methods/random_labels - [notice] Building container 'label_projection/control_methods_random_labels:dev' with Dockerfile - [notice] Building container 'common/data_processing_dataset_concatenate:dev' with Dockerfile - [notice] Building container 'label_projection/metrics_accuracy:dev' with Dockerfile - ... - -Viash will build a whole namespace (`ns`) into executables and Nextflow pipelines into the `target/docker` and `target/nextflow` folders respectively. -By adding the `-q/--query` flag, you can filter which components to build using a regex. -By adding the `--parallel` flag, these components are built in parallel (otherwise it will take a really long time). -The flag `--setup cachedbuild` will automatically start building Docker containers for each of these methods. - -The command might take a while to run, since it is building a docker container for each of the components. - -**Step 3, run the pipeline with nextflow.** To do so, run the bash script located at `src/tasks/label_projection/workflows/run_nextflow.sh`: - -```bash -src/tasks/label_projection/workflows/run/run_test.sh -``` - - N E X T F L O W ~ version 22.04.5 - Launching `src/tasks/label_projection/workflows/run/main.nf` [pensive_turing] DSL2 - revision: 16b7b0c332 - executor > local (28) - [f6/f89435] process > run_wf:run_methods:true_labels:true_labels_process (pancreas.true_labels) [100%] 1 of 1 ✔ - [ed/d674a2] process > run_wf:run_methods:majority_vote:majority_vote_process (pancreas.majority_vote) [100%] 1 of 1 ✔ - [15/f0a427] process > run_wf:run_methods:random_labels:random_labels_process (pancreas.random_labels) [100%] 1 of 1 ✔ - [02/969d05] process > run_wf:run_methods:knn:knn_process (pancreas.knn) [100%] 1 of 1 ✔ - [90/5fdf9a] process > run_wf:run_methods:mlp:mlp_process (pancreas.mlp) [100%] 1 of 1 ✔ - [c7/dee2e5] process > run_wf:run_methods:logistic_regression:logistic_regression_process (pancreas.logistic_regression) [100%] 1 of 1 ✔ - [83/3ba0c9] process > run_wf:run_methods:scanvi:scanvi_process (pancreas.scanvi) [100%] 1 of 1 ✔ - [e3/2c298e] process > run_wf:run_methods:seurat_transferdata:seurat_transferdata_process (pancreas.seurat_transferdata) [100%] 1 of 1 ✔ - [d6/7212ab] process > run_wf:run_methods:xgboost:xgboost_process (pancreas.xgboost) [100%] 1 of 1 ✔ - [b6/7dc1a7] process > run_wf:run_metrics:accuracy:accuracy_process (pancreas.scanvi) [100%] 9 of 9 ✔ - [be/7d4da4] process > run_wf:run_metrics:f1:f1_process (pancreas.scanvi) [100%] 9 of 9 ✔ - [89/dcd77a] process > run_wf:aggregate_results:extract_scores:extract_scores_process (combined) [100%] 1 of 1 ✔ - -## Project structure - -High level overview: - . - ├── bin Helper scripts for building the project and developing a new component. - ├── resources_test Datasets for testing components. If you don't have this folder, run **Step 1** above. - ├── src Source files for each component in the pipeline. - │ ├── common Common processing components. - │ ├── datasets Components and pipelines for building the 'Common datasets' - │ ├── label_projection Source files related to the 'Label projection' task. - │ └── ... Other tasks. - └── target Executables generated by viash based on the components listed under `src/`. - ├── docker Bash executables which can be used from a terminal. - └── nextflow Nextflow modules which can be used as a standalone pipeline or as part of a bigger pipeline. - -Detailed overview of a task folder (e.g. `src/tasks/label_projection`): - - src/tasks/label_projection/ - ├── api Specs for the components in this task. - ├── control_methods Control methods which serve as quality control checks for the benchmark. - ├── docs Task documentation - ├── methods Label projection method components. - ├── metrics Label projection metric components. - ├── resources_scripts The scripts needed to run the benchmark. - ├── resources_test_scripts The scripts needed to generate the test resources (which are needed for unit testing). - ├── process_dataset A component that masks a common dataset for use in the benchmark - └── workflows The benchmarking workflow. - - -Detailed overview of the `src/datasets` folder: - - src/datasets/ - ├── api Specs for the data loaders and normalisation methods. - ├── loaders Components for ingesting datasets from a source. - ├── normalization Normalization method components. - ├── processors Other preprocessing components (e.g. HVG and PCA). - ├── resource_scripts The scripts needed to generate the common datasets. - ├── resource_test_scripts The scripts needed to generate the test resources (which are needed for unit testing). - └── workflows The workflow which generates the common datasets. - -## Adding a Viash component - -[Viash](https://viash.io) allows you to create pipelines -in Bash or Nextflow by wrapping Python, R, or Bash scripts into reusable components. - - -You can start creating a new component by [creating a Viash component](https://viash.io/guide/component/creation/docker.html). - - -```{bash, include=FALSE} - -mkdir -p src/tasks/label_projection/methods/foo - -cat > src/tasks/label_projection/methods/foo/config.vsh.yaml << HERE -__merge__: ../../api/comp_method.yaml -functionality: - name: "foo" - namespace: "label_projection/methods" - # A multiline description of your method. - description: "Todo: fill in" - info: - type: method - - # a short label of your method - label: Foo - - # A multiline description of your method. - description: "Todo: fill in" - - # A short summary of the method description. - summary: "Todo: fill in" - - # Add the bibtex reference to the "src/common/library.bib" if it is not already there. - reference: "cover1967nearest" - - repository_url: "https://github.com/openproblems-bio/openproblems-v2" - documentation_url: "https://openproblems.bio/documentation/" - preferred_normalization: log_cp10k - resources: - - type: python_script - path: script.py -platforms: - - type: docker - image: openproblems/base_python:1.0.0 - setup: - - type: python - packages: [scikit-learn] - - type: nextflow - directives: - label: [midtime, midmem, lowcpu] -HERE - -cat > src/tasks/label_projection/methods/foo/script.py << HERE -import anndata as ad -import numpy as np - -## VIASH START -# This code-block will automatically be replaced by Viash at runtime. -par = { - 'input_train': 'resources_test/label_projection/pancreas/train.h5ad', - 'input_test': 'resources_test/label_projection/pancreas/test.h5ad', - 'output': 'output.h5ad' -} -meta = { - 'functionality_name': 'foo' -} -## VIASH END - -print("Load data", flush=True) -input_train = ad.read_h5ad(par['input_train']) -input_test = ad.read_h5ad(par['input_test']) - -print("Create predictions", flush=True) -input_test.obs["label_pred"] = "foo" - -print("Add method name to uns", flush=True) -input_test.uns["method_id"] = meta["functionality_name"] - -print("Write output to file", flush=True) -input_test.write_h5ad(par["output"], compression="gzip") -HERE -``` - -For example, to create a new Python-based method named `foo`, create a Viash config at `src/tasks/label_projection/methods/foo/config.vsh.yaml`: - -```{embed lang="yaml"} -src/tasks/label_projection/methods/foo/config.vsh.yaml -``` - -And create a script at `src/tasks/label_projection/methods/foo/script.py`: - -```{embed lang="python"} -src/tasks/label_projection/methods/foo/script.py -``` - - -## Running a component from CLI - -You can view the interface of the executable by running the executable with the `-h` or `--help` parameter. - -```{bash} -viash run src/tasks/label_projection/methods/foo/config.vsh.yaml -- --help -``` - -Before running a new component, youy will need to create the docker container: - -```{bash} -viash run src/tasks/label_projection/methods/foo/config.vsh.yaml -- ---setup cachedbuild - -``` - -You can **run the component** as follows: - -```{bash} -viash run src/tasks/label_projection/methods/foo/config.vsh.yaml -- \ - --input_train resources_test/label_projection/pancreas/train.h5ad \ - --input_test resources_test/label_projection/pancreas/test.h5ad \ - --output resources_test/label_projection/pancreas/prediction.h5ad -``` - -## Building a component - -`viash` has several helper functions to help you quickly develop a component. - -With **`viash build`**, you can turn the component into a standalone executable. -This standalone executable you can give to somebody else, and they will be able to -run it, provided that they have Bash and Docker installed. - -```{bash} -viash build src/tasks/label_projection/methods/foo/config.vsh.yaml \ - -o target/docker/label_projection/methods/foo -``` - -:::{.callout-note} -The `viash ns build` component does a much better job of setting up -a collection of components. -::: - -You can now view the same interface of the executable by running the executable with the `-h` parameter. - -```{bash} -target/docker/label_projection/methods/foo/foo -h -``` - -Or **run the component** as follows: - -```{bash} -target/docker/label_projection/methods/foo/foo \ - --input_train resources_test/label_projection/pancreas/train.h5ad \ - --input_test resources_test/label_projection/pancreas/test.h5ad \ - --output resources_test/label_projection/pancreas/prediction.h5ad -``` - - -## Unit testing a component - -The [method API specifications](src/tasks/label_projection/api/comp_method.yaml) comes with a generic unit test for free. -This means you can unit test your component using the **`viash test`** command. - -```{bash} -viash test src/tasks/label_projection/methods/foo/config.vsh.yaml -``` - -```{bash include=FALSE} -cat > src/tasks/label_projection/methods/foo/script.py << HERE -import anndata as ad -import numpy as np - -## VIASH START -# This code-block will automatically be replaced by Viash at runtime. -par = { - 'input_train': 'resources_test/label_projection/pancreas/train.h5ad', - 'input_test': 'resources_test/label_projection/pancreas/test.h5ad', - 'output': 'output.h5ad' -} -meta = { - 'functionality_name': 'foo' -} -## VIASH END - -print("Load data", flush=True) -input_train = ad.read_h5ad(par['input_train']) -input_test = ad.read_h5ad(par['input_test']) - -print("Not creating any predictions!!!", flush=True) -# input_test.obs["label_pred"] = "foo" - -print("Not adding method name to uns!!!", flush=True) -# input_test.uns["method_id"] = meta["functionality_name"] - -print("Write output to file", flush=True) -input_test.write_h5ad(par["output"], compression="gzip") -HERE -``` - -Let's introduce a bug in the script and try running the test again. For instance: - -```{embed lang="python"} -src/tasks/label_projection/methods/foo/script.py -``` - -If we now run the test, we should get an error since we didn't create all of the required output slots. - -```{bash error=TRUE} -viash test src/tasks/label_projection/methods/foo/config.vsh.yaml -``` - - -## More information - -The [Viash reference docs](https://viash.io/reference/config/) page provides information on all of the available fields in a Viash config, and the [Guide](https://viash.io/guide/) will help you get started with creating components from scratch. - - - - -```{bash, echo=FALSE} -rm -r src/tasks/label_projection/methods/foo target/docker/label_projection/methods/foo -``` - -## Branch Naming Conventions - -### Category - -A git branch should start with a category. Pick one of these: feature, bugfix, hotfix, or test. - -* `feature` is for adding, refactoring or removing a feature -* `bugfix` is for fixing a bug -* `hotfix` is for changing code with a temporary solution and/or without following the usual process (usually because of an emergency) -* `test` is for experimenting outside of an issue/ticket -* `doc` is for adding, changing or removing documentation - -### Reference - -After the category, there should be a "`/`" followed by the reference of the issue/ticket/task you are working on. If there's no reference, just add no-ref. With task it is meant as benchmarking task e.g. batch_integration - -### Description - -After the reference, there should be another "`/`" followed by a description which sums up the purpose of this specific branch. This description should be short and "kebab-cased". - -By default, you can use the title of the issue/ticket you are working on. Just replace any special character by "`-`". - -### To sum up, follow this pattern when branching: - -```bash -git branch -``` - -### Examples - -* You need to add, refactor or remove a feature: `git branch feature/issue-42/create-new-button-component` -* You need to fix a bug: `git branch bugfix/issue-342/button-overlap-form-on-mobile` -* You need to fix a bug really fast (possibly with a temporary solution): `git branch hotfix/no-ref/registration-form-not-working` -* You need to experiment outside of an issue/ticket: `git branch test/no-ref/refactor-components-with-atomic-design` - -### References - -* [a-simplified-convention-for-naming-branches-and-commits-in-git](https://dev.to/varbsan/a-simplified-convention-for-naming-branches-and-commits-in-git-il4) \ No newline at end of file diff --git a/src/common/create_component/config.vsh.yaml b/src/common/create_component/config.vsh.yaml index 5c829462ad..b8dc748fb6 100644 --- a/src/common/create_component/config.vsh.yaml +++ b/src/common/create_component/config.vsh.yaml @@ -56,9 +56,9 @@ functionality: - type: python_script path: test.py - path: /src - dest: openproblems-v2/src + dest: openproblems/src - path: /_viash.yaml - dest: openproblems-v2/_viash.yaml + dest: openproblems/_viash.yaml platforms: - type: docker image: python:3.10-slim diff --git a/src/common/create_component/test.py b/src/common/create_component/test.py index 16da1bd854..a53e54a18e 100644 --- a/src/common/create_component/test.py +++ b/src/common/create_component/test.py @@ -9,7 +9,7 @@ } ## VIASH END -opv2 = f"{meta['resources_dir']}/openproblems-v2" +opv2 = f"{meta['resources_dir']}/openproblems" output_path = f"{opv2}/src/tasks/label_projection/methods/test_method" cmd = [ diff --git a/src/common/create_task_readme/config.vsh.yaml b/src/common/create_task_readme/config.vsh.yaml index d268974ce8..cff0917b0d 100644 --- a/src/common/create_task_readme/config.vsh.yaml +++ b/src/common/create_task_readme/config.vsh.yaml @@ -25,7 +25,7 @@ functionality: name: --github_url description: | URL to the GitHub repository. Needed for linking to the source code. - default: "https://github.com/openproblems-bio/openproblems-v2/tree/main/" + default: "https://github.com/openproblems-bio/openproblems/tree/main/" - name: Outputs arguments: - type: file @@ -43,9 +43,9 @@ functionality: - type: r_script path: test.R - path: /src - dest: openproblems-v2/src + dest: openproblems/src - path: /_viash.yaml - dest: openproblems-v2/_viash.yaml + dest: openproblems/_viash.yaml platforms: - type: docker image: openproblems/base_r:1.0.0 diff --git a/src/common/create_task_readme/script.R b/src/common/create_task_readme/script.R index 55388ea7ed..35320e4d97 100644 --- a/src/common/create_task_readme/script.R +++ b/src/common/create_task_readme/script.R @@ -8,7 +8,7 @@ par <- list( "task_dir" = "src/tasks/batch_integration", "output" = "src/tasks/batch_integration/README.md", "viash_yaml" = "_viash.yaml", - "github_url" = "https://github.com/openproblems-bio/openproblems-v2/tree/main/" + "github_url" = "https://github.com/openproblems-bio/openproblems/tree/main/" ) meta <- list( "resources_dir" = "src/common/helper_functions", diff --git a/src/common/create_task_readme/test.R b/src/common/create_task_readme/test.R index 9af1fe9738..3a981fe7ca 100644 --- a/src/common/create_task_readme/test.R +++ b/src/common/create_task_readme/test.R @@ -3,7 +3,7 @@ requireNamespace("assertthat", quietly = TRUE) ## VIASH START ## VIASH END -opv2 <- paste0(meta$resources_dir, "/openproblems-v2") +opv2 <- paste0(meta$resources_dir, "/openproblems") output_path <- "output.md" cat(">> Running the script as test\n") diff --git a/src/common/helper_functions/read_api_files.R b/src/common/helper_functions/read_api_files.R index be602b58c4..f2cf49b2f8 100644 --- a/src/common/helper_functions/read_api_files.R +++ b/src/common/helper_functions/read_api_files.R @@ -232,7 +232,7 @@ render_component <- function(spec) { strip_margin(glue::glue(" §## Component type: {spec$info$label} § - §Path: [`src/{spec$info$namespace}`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/{spec$info$namespace}) + §Path: [`src/{spec$info$namespace}`](https://github.com/openproblems-bio/openproblems/tree/main/src/{spec$info$namespace}) § §{spec$info$summary} § diff --git a/src/common/ontology/check_obsolete_terms/config.vsh.yaml b/src/common/ontology/check_obsolete_terms/config.vsh.yaml deleted file mode 100644 index fc006f6cf9..0000000000 --- a/src/common/ontology/check_obsolete_terms/config.vsh.yaml +++ /dev/null @@ -1,76 +0,0 @@ -functionality: - status: disabled - name: check_obsolete_terms - namespace: common/ontology - description: | - Check for obsolete ontology terms in the dataset. - argument_groups: - - name: Inputs - arguments: - - name: "--input" - type: file - description: "Input h5ad file." - required: true - direction: input - example: dataset.h5ad - - name: "--struct" - type: string - description: "In which struct to look for the term." - required: true - direction: input - example: "obs" - - name: "--input_term" - type: string - description: "In which field to look for the term." - required: true - direction: input - example: "cell_type_ontology_term_id" - - name: Ontology - arguments: - - name: "--ontology" - type: file - description: "Ontology to check." - required: true - direction: input - example: cl.obo - - name: Arguments - arguments: - - name: "--obsolete_as_na" - type: boolean - description: "Whether to replace obsolete terms with NA." - default: true - - name: Outputs - arguments: - - name: "--output" - type: file - description: Output h5ad file. - direction: output - example: output.h5ad - - name: "--output_term" - type: string - description: "In which field to store the updated term." - required: true - example: "cell_type_ontology_term_id" - - name: "--output_name" - type: string - description: "In which field to store the updated term name." - required: true - example: "cell_type" - - name: "--output_obsolete" - type: string - description: "In which field to store whether a term is obsolete." - required: true - example: "cell_type_ontology_obsolete" - resources: - - type: r_script - path: script.R - test_resources: - - type: r_script - path: test.R - - path: /resources_test/common/cellxgene_census -platforms: - - type: docker - image: openproblems/base_r:1.0.0 - setup: - - type: r - packages: [ dplyr, tidyr, tibble, ontologyIndex, processx ] \ No newline at end of file diff --git a/src/common/ontology/check_obsolete_terms/script.R b/src/common/ontology/check_obsolete_terms/script.R deleted file mode 100644 index bc1ef0ccb7..0000000000 --- a/src/common/ontology/check_obsolete_terms/script.R +++ /dev/null @@ -1,63 +0,0 @@ -library(dplyr, warn.conflicts = FALSE) -library(tidyr, warn.conflicts = FALSE) -library(tibble, warn.conflicts = FALSE) -library(ontologyIndex, warn.conflicts = FALSE) - -## VIASH START -par <- list( - input = "resources_test/common/cellxgene_census/dataset.h5ad", - ontology = "resources_test/common/cellxgene_census/cl.obo", - input_term = "cell_type_ontology_term_id", - struct = "obs", - output = "output.h5ad", - output_term = "cell_type_ontology_term_id", - output_name = "cell_type", - output_obsolete = "cell_type_ontology_obsolete", - obsolete_as_na = TRUE -) -## VIASH END - -cat("Read ontology\n") -ont <- ontologyIndex::get_ontology( - par$ontology, - extract_tags = "everything" -) -ont_tib <- ont %>% - as.data.frame %>% - select(id, name, obsolete, replaced_by) %>% - as_tibble - -cat("Read anndata\n") -adata <- anndata::read_h5ad(par$input, backed = "r") - -cat("Find terms\n") -term_ids <- adata[[par$struct]][[par$input_term]] - -unique_term_ids <- as.character(unique(term_ids)) - -cat("Look for obsolete or replaced terms\n") -ont_map <- ont_tib %>% - slice(match(unique_term_ids, id)) %>% - transmute( - orig_id = id, - id = case_when( - !obsolete ~ id, - replaced_by != "" ~ replaced_by, - rep(par$obsolete_as_na, length(id)) ~ rep(NA_character_, length(id)), - TRUE ~ id - ) - ) %>% - left_join(ont_tib %>% select(id, name, obsolete), by = "id") - -cat("Store new columns in data structure\n") -new_data <- ont_map %>% slice(match(term_ids, orig_id)) -adata[[par$struct]][[par$output_term]] <- new_data$id -adata[[par$struct]][[par$output_name]] <- new_data$name -adata[[par$struct]][[par$output_obsolete]] <- ifelse( - !is.na(new_data$obsolete), - new_data$obsolete, - TRUE -) - -cat("Write to file\n") -anndata::write_h5ad(adata, par$output) diff --git a/src/common/ontology/check_obsolete_terms/test.R b/src/common/ontology/check_obsolete_terms/test.R deleted file mode 100644 index 5e3c582021..0000000000 --- a/src/common/ontology/check_obsolete_terms/test.R +++ /dev/null @@ -1,54 +0,0 @@ -library(assertthat) - -## VIASH START -meta <- list( - executable = "target/docker/common/ontology/check_obsolete_terms", - resources_dir = "resources_test/common/" -) -## VIASH END - -input_file <- paste0(meta$resources_dir, "/cellxgene_census/dataset.h5ad") -ontology_file <- paste0(meta$resources_dir, "/cellxgene_census/cl.obo") -temp_file <- tempfile(fileext = ".h5ad") -temp2_file <- tempfile(fileext = ".h5ad") - -# add obsolete terms to the dataset -input <- anndata::read_h5ad(input_file) -input$obs$cell_type_ontology_term_id <- as.character(input$obs$cell_type_ontology_term_id) -input$obs$cell_type_ontology_term_id[1:3] <- "CL:0000375" # obsolete, replaced by 'CL:0007010' -input$obs$cell_type_ontology_term_id[4:6] <- "CL:0000399" # obsolete, removed -input$obs$cell_type_ontology_term_id[7:9] <- "CL:0007011" # not obsolete -zzz <- input$write_h5ad(temp_file) - -# run component -zzz <- processx::run( - meta$executable, - c( - "--input", temp_file, - "--struct", "obs", - "--input_term", "cell_type_ontology_term_id", - "--ontology", ontology_file, - "--output", temp2_file, - "--output_term", "cell_type_ontology_term_id_new", - "--output_name", "cell_type_new", - "--output_obsolete", "cell_type_obsolete_new" - ), - echo = TRUE -) - -# check output -output <- anndata::read_h5ad(temp2_file) - -print(output$obs[1:10, , drop = FALSE]) - -assert_that( - all(output$obs$cell_type_ontology_term_id_new[1:3] == "CL:0007010"), - all(is.na(output$obs$cell_type_ontology_term_id_new[4:6])), - all(output$obs$cell_type_ontology_term_id_new[7:9] == "CL:0007011"), - all(output$obs$cell_type_new[1:3] == "preosteoblast"), - all(is.na(output$obs$cell_type_new[4:6])), - all(output$obs$cell_type_new[7:9] == "enteric neuron"), - all(!output$obs$cell_type_obsolete_new[1:3]), - all(output$obs$cell_type_obsolete_new[4:6]), - all(!output$obs$cell_type_obsolete_new[7:9]) -) diff --git a/src/common/process_task_results/api/get_info.yaml b/src/common/process_task_results/api/get_info.yaml index 117504cc75..9691936615 100644 --- a/src/common/process_task_results/api/get_info.yaml +++ b/src/common/process_task_results/api/get_info.yaml @@ -18,6 +18,6 @@ functionality: - type: python_script path: /src/common/comp_tests/check_get_info.py - path: /src - dest: openproblems-v2/src + dest: openproblems/src - path: /_viash.yaml - dest: openproblems-v2/_viash.yaml \ No newline at end of file + dest: openproblems/_viash.yaml \ No newline at end of file diff --git a/src/common/process_task_results/get_task_info/script.R b/src/common/process_task_results/get_task_info/script.R index cfe529edfc..71f1cb777a 100644 --- a/src/common/process_task_results/get_task_info/script.R +++ b/src/common/process_task_results/get_task_info/script.R @@ -20,7 +20,7 @@ out <- list( task_name = info$label, task_summary = info$summary, task_description = paste0(info$motivation, "\n\n", info$description), - repo = "openproblems-bio/openproblems-v2", + repo = "openproblems-bio/openproblems", authors = info$authors ) diff --git a/src/common/process_task_results/run/run_nf_tower_test.sh b/src/common/process_task_results/run/run_nf_tower_test.sh index 95fa080f12..ca74e357a1 100644 --- a/src/common/process_task_results/run/run_nf_tower_test.sh +++ b/src/common/process_task_results/run/run_nf_tower_test.sh @@ -28,7 +28,7 @@ process { HERE -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ +tw launch https://github.com/openproblems-bio/openproblems.git \ --revision main_build \ --pull-latest \ --main-script target/nextflow/common/workflows/transform_meta/main.nf \ diff --git a/src/datasets/resource_scripts/cellxgene_census.sh b/src/datasets/resource_scripts/cellxgene_census.sh index f0d93c9210..5d6181f91e 100755 --- a/src/datasets/resource_scripts/cellxgene_census.sh +++ b/src/datasets/resource_scripts/cellxgene_census.sh @@ -142,7 +142,7 @@ process { } HERE -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ +tw launch https://github.com/openproblems-bio/openproblems.git \ --revision main_build \ --pull-latest \ --main-script target/nextflow/datasets/workflows/process_cellxgene_census/main.nf \ diff --git a/src/datasets/resource_scripts/dataset_info.sh b/src/datasets/resource_scripts/dataset_info.sh index 6ec2de9963..04c032916f 100755 --- a/src/datasets/resource_scripts/dataset_info.sh +++ b/src/datasets/resource_scripts/dataset_info.sh @@ -31,7 +31,7 @@ process { } HERE -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ +tw launch https://github.com/openproblems-bio/openproblems.git \ --revision main_build \ --entry-name auto \ --pull-latest \ diff --git a/src/datasets/resource_scripts/openproblems_neurips2021_multimodal.sh b/src/datasets/resource_scripts/openproblems_neurips2021_multimodal.sh index 8fd7e3a72d..a306ba2ef8 100755 --- a/src/datasets/resource_scripts/openproblems_neurips2021_multimodal.sh +++ b/src/datasets/resource_scripts/openproblems_neurips2021_multimodal.sh @@ -35,7 +35,7 @@ output_state: '$id/state.yaml' publish_dir: s3://openproblems-data/resources/datasets HERE -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ +tw launch https://github.com/openproblems-bio/openproblems.git \ --revision main_build \ --pull-latest \ --main-script target/nextflow/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf \ diff --git a/src/datasets/resource_scripts/openproblems_neurips2022_pbmc.sh b/src/datasets/resource_scripts/openproblems_neurips2022_pbmc.sh index 56b61ca104..e3e6783a8e 100755 --- a/src/datasets/resource_scripts/openproblems_neurips2022_pbmc.sh +++ b/src/datasets/resource_scripts/openproblems_neurips2022_pbmc.sh @@ -46,7 +46,7 @@ process { } HERE -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ +tw launch https://github.com/openproblems-bio/openproblems.git \ --revision main_build \ --pull-latest \ --main-script target/nextflow/datasets/workflows/process_openproblems_neurips2022_pbmc/main.nf \ diff --git a/src/datasets/resource_scripts/openproblems_v1.sh b/src/datasets/resource_scripts/openproblems_v1.sh index 1a01e2120e..8d40e57c46 100755 --- a/src/datasets/resource_scripts/openproblems_v1.sh +++ b/src/datasets/resource_scripts/openproblems_v1.sh @@ -171,7 +171,7 @@ process { } HERE -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ +tw launch https://github.com/openproblems-bio/openproblems.git \ --revision main_build \ --pull-latest \ --main-script target/nextflow/datasets/workflows/process_openproblems_v1/main.nf \ diff --git a/src/datasets/resource_scripts/openproblems_v1_multimodal.sh b/src/datasets/resource_scripts/openproblems_v1_multimodal.sh index 3efb960c45..2d516a8ccb 100755 --- a/src/datasets/resource_scripts/openproblems_v1_multimodal.sh +++ b/src/datasets/resource_scripts/openproblems_v1_multimodal.sh @@ -74,7 +74,7 @@ process { } HERE -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ +tw launch https://github.com/openproblems-bio/openproblems.git \ --revision main_build \ --pull-latest \ --main-script target/nextflow/datasets/workflows/process_openproblems_v1_multimodal/main.nf \ diff --git a/src/datasets/resource_scripts/tenx_visium.sh b/src/datasets/resource_scripts/tenx_visium.sh index 7993cebd4b..d5b54e7ef5 100755 --- a/src/datasets/resource_scripts/tenx_visium.sh +++ b/src/datasets/resource_scripts/tenx_visium.sh @@ -306,7 +306,7 @@ process { } HERE -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ +tw launch https://github.com/openproblems-bio/openproblems.git \ --revision integration_build \ --pull-latest \ --main-script target/nextflow/datasets/workflows/process_tenx_visium/main.nf \ diff --git a/src/datasets/resource_scripts/zenodo_spatial.sh.sh b/src/datasets/resource_scripts/zenodo_spatial.sh.sh index 192cb8cc9c..7842b4368f 100755 --- a/src/datasets/resource_scripts/zenodo_spatial.sh.sh +++ b/src/datasets/resource_scripts/zenodo_spatial.sh.sh @@ -404,7 +404,7 @@ process { } HERE -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ +tw launch https://github.com/openproblems-bio/openproblems.git \ --revision main_build \ --pull-latest \ --main-script target/nextflow/datasets/workflows/process_zenodo_spatial/main.nf \ diff --git a/src/datasets/resource_scripts/zenodo_spatial_slidetags.sh b/src/datasets/resource_scripts/zenodo_spatial_slidetags.sh index d8654ce439..5ab4962240 100755 --- a/src/datasets/resource_scripts/zenodo_spatial_slidetags.sh +++ b/src/datasets/resource_scripts/zenodo_spatial_slidetags.sh @@ -72,7 +72,7 @@ process { } HERE -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ +tw launch https://github.com/openproblems-bio/openproblems.git \ --revision main_build \ --pull-latest \ --main-script target/nextflow/datasets/workflows/process_zenodo_spatial_slidetags/main.nf \ diff --git a/src/datasets/resource_test_scripts/neurips2021_bmmc.sh b/src/datasets/resource_test_scripts/neurips2021_bmmc.sh index 7922f634cb..98644d9dbf 100755 --- a/src/datasets/resource_test_scripts/neurips2021_bmmc.sh +++ b/src/datasets/resource_test_scripts/neurips2021_bmmc.sh @@ -58,7 +58,7 @@ nextflow run . \ -params-file "$params_file" \ -c src/wf_utils/labels.config -# tw launch https://github.com/openproblems-bio/openproblems-v2.git \ +# tw launch https://github.com/openproblems-bio/openproblems.git \ # --revision main_build \ # --main-script target/nextflow/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf \ # --workspace 53907369739130 \ diff --git a/src/datasets/resource_test_scripts/neurips2022_pbmc.sh b/src/datasets/resource_test_scripts/neurips2022_pbmc.sh index ef2e0523e1..b62e6f40e1 100755 --- a/src/datasets/resource_test_scripts/neurips2022_pbmc.sh +++ b/src/datasets/resource_test_scripts/neurips2022_pbmc.sh @@ -60,7 +60,7 @@ process { HERE -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ +tw launch https://github.com/openproblems-bio/openproblems.git \ --revision main_build \ --pull-latest \ --main-script target/nextflow/datasets/workflows/process_openproblems_neurips2022_pbmc/main.nf \ diff --git a/src/tasks/batch_integration/README.md b/src/tasks/batch_integration/README.md index 7d525e9fc8..073a654508 100644 --- a/src/tasks/batch_integration/README.md +++ b/src/tasks/batch_integration/README.md @@ -5,7 +5,7 @@ Remove unwanted batch effects from scRNA data while retaining biologically meaningful variation. Path: -[`src/tasks/batch_integration`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/tasks/batch_integration) +[`src/tasks/batch_integration`](https://github.com/openproblems-bio/openproblems/tree/main/src/tasks/batch_integration) ## Motivation @@ -151,7 +151,7 @@ Slot description: ## Component type: Data processor Path: -[`src/batch_integration`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/batch_integration) +[`src/batch_integration`](https://github.com/openproblems-bio/openproblems/tree/main/src/batch_integration) A label projection dataset processor. @@ -265,7 +265,7 @@ Slot description: ## Component type: Control method (embedding) Path: -[`src/batch_integration/control_methods`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/batch_integration/control_methods) +[`src/batch_integration/control_methods`](https://github.com/openproblems-bio/openproblems/tree/main/src/batch_integration/control_methods) A batch integration embedding control method. @@ -283,7 +283,7 @@ Arguments: ## Component type: Control method (graph) Path: -[`src/batch_integration/control_methods`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/batch_integration/control_methods) +[`src/batch_integration/control_methods`](https://github.com/openproblems-bio/openproblems/tree/main/src/batch_integration/control_methods) A batch integration graph control method. @@ -301,7 +301,7 @@ Arguments: ## Component type: Method (embedding) Path: -[`src/batch_integration/methods`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/batch_integration/methods) +[`src/batch_integration/methods`](https://github.com/openproblems-bio/openproblems/tree/main/src/batch_integration/methods) A batch integration embedding method. @@ -319,7 +319,7 @@ Arguments: ## Component type: Method (feature) Path: -[`src/batch_integration/methods`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/batch_integration/methods) +[`src/batch_integration/methods`](https://github.com/openproblems-bio/openproblems/tree/main/src/batch_integration/methods) A batch integration feature method. @@ -337,7 +337,7 @@ Arguments: ## Component type: Method (graph) Path: -[`src/batch_integration/methods`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/batch_integration/methods) +[`src/batch_integration/methods`](https://github.com/openproblems-bio/openproblems/tree/main/src/batch_integration/methods) A batch integration graph method. @@ -355,7 +355,7 @@ Arguments: ## Component type: Metric (embedding) Path: -[`src/batch_integration/metrics`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/batch_integration/metrics) +[`src/batch_integration/metrics`](https://github.com/openproblems-bio/openproblems/tree/main/src/batch_integration/metrics) A batch integration embedding metric. @@ -374,7 +374,7 @@ Arguments: ## Component type: Metric (feature) Path: -[`src/batch_integration/metrics`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/batch_integration/metrics) +[`src/batch_integration/metrics`](https://github.com/openproblems-bio/openproblems/tree/main/src/batch_integration/metrics) A batch integration feature metric. @@ -393,7 +393,7 @@ Arguments: ## Component type: Metric (graph) Path: -[`src/batch_integration/metrics`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/batch_integration/metrics) +[`src/batch_integration/metrics`](https://github.com/openproblems-bio/openproblems/tree/main/src/batch_integration/metrics) A batch integration graph metric. @@ -536,7 +536,7 @@ Slot description: ## Component type: Embedding to Graph Path: -[`src/batch_integration/transformers`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/batch_integration/transformers) +[`src/batch_integration/transformers`](https://github.com/openproblems-bio/openproblems/tree/main/src/batch_integration/transformers) Transform an embedding to a graph output. @@ -554,7 +554,7 @@ Arguments: ## Component type: Feature to Embedding Path: -[`src/batch_integration/transformers`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/batch_integration/transformers) +[`src/batch_integration/transformers`](https://github.com/openproblems-bio/openproblems/tree/main/src/batch_integration/transformers) Transform a feature output to an embedding. diff --git a/src/tasks/batch_integration/resources_scripts/process_datasets.sh b/src/tasks/batch_integration/resources_scripts/process_datasets.sh index 97e6b2c61c..b49c203af8 100755 --- a/src/tasks/batch_integration/resources_scripts/process_datasets.sh +++ b/src/tasks/batch_integration/resources_scripts/process_datasets.sh @@ -21,7 +21,7 @@ process { } HERE -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ +tw launch https://github.com/openproblems-bio/openproblems.git \ --revision main_build \ --pull-latest \ --main-script target/nextflow/batch_integration/workflows/process_datasets/main.nf \ diff --git a/src/tasks/batch_integration/resources_scripts/run_benchmark.sh b/src/tasks/batch_integration/resources_scripts/run_benchmark.sh index f48a5ccdd1..cd83810680 100755 --- a/src/tasks/batch_integration/resources_scripts/run_benchmark.sh +++ b/src/tasks/batch_integration/resources_scripts/run_benchmark.sh @@ -10,7 +10,7 @@ output_state: "state.yaml" publish_dir: "$publish_dir" HERE -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ +tw launch https://github.com/openproblems-bio/openproblems.git \ --revision main_build \ --pull-latest \ --main-script target/nextflow/batch_integration/workflows/run_benchmark/main.nf \ diff --git a/src/tasks/batch_integration/resources_scripts/run_benchmark_test.sh b/src/tasks/batch_integration/resources_scripts/run_benchmark_test.sh index b9b80a38ea..eca3049d3a 100755 --- a/src/tasks/batch_integration/resources_scripts/run_benchmark_test.sh +++ b/src/tasks/batch_integration/resources_scripts/run_benchmark_test.sh @@ -13,7 +13,7 @@ process { } HERE -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ +tw launch https://github.com/openproblems-bio/openproblems.git \ --revision main_build \ --pull-latest \ --main-script target/nextflow/batch_integration/workflows/run_benchmark/main.nf \ diff --git a/src/tasks/denoising/README.md b/src/tasks/denoising/README.md index da9d9b1912..5f33715180 100644 --- a/src/tasks/denoising/README.md +++ b/src/tasks/denoising/README.md @@ -4,7 +4,7 @@ Removing noise in sparse single-cell RNA-sequencing count data Path: -[`src/tasks/denoising`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/tasks/denoising) +[`src/tasks/denoising`](https://github.com/openproblems-bio/openproblems/tree/main/src/tasks/denoising) ## Motivation @@ -162,7 +162,7 @@ Slot description: ## Component type: Data processor Path: -[`src/denoising`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/denoising) +[`src/denoising`](https://github.com/openproblems-bio/openproblems/tree/main/src/denoising) A denoising dataset processor. @@ -242,7 +242,7 @@ Slot description: ## Component type: Control method Path: -[`src/denoising/control_methods`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/denoising/control_methods) +[`src/denoising/control_methods`](https://github.com/openproblems-bio/openproblems/tree/main/src/denoising/control_methods) Quality control methods for verifying the pipeline. @@ -261,7 +261,7 @@ Arguments: ## Component type: Method Path: -[`src/denoising/methods`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/denoising/methods) +[`src/denoising/methods`](https://github.com/openproblems-bio/openproblems/tree/main/src/denoising/methods) A denoising method. @@ -279,7 +279,7 @@ Arguments: ## Component type: Metric Path: -[`src/denoising/metrics`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/denoising/metrics) +[`src/denoising/metrics`](https://github.com/openproblems-bio/openproblems/tree/main/src/denoising/metrics) A denoising metric. diff --git a/src/tasks/denoising/resources_scripts/process_datasets.sh b/src/tasks/denoising/resources_scripts/process_datasets.sh index 44060a8f66..873b9fb0b4 100755 --- a/src/tasks/denoising/resources_scripts/process_datasets.sh +++ b/src/tasks/denoising/resources_scripts/process_datasets.sh @@ -22,7 +22,7 @@ process { } HERE -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ +tw launch https://github.com/openproblems-bio/openproblems.git \ --revision main_build \ --pull-latest \ --main-script target/nextflow/denoising/workflows/process_datasets/main.nf \ diff --git a/src/tasks/denoising/resources_scripts/run_benchmark.sh b/src/tasks/denoising/resources_scripts/run_benchmark.sh index 983c42cc56..8e38568ac8 100755 --- a/src/tasks/denoising/resources_scripts/run_benchmark.sh +++ b/src/tasks/denoising/resources_scripts/run_benchmark.sh @@ -11,7 +11,7 @@ output_state: "state.yaml" publish_dir: "$publish_dir" HERE -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ +tw launch https://github.com/openproblems-bio/openproblems.git \ --revision main_build \ --pull-latest \ --main-script target/nextflow/denoising/workflows/run_benchmark/main.nf \ diff --git a/src/tasks/denoising/resources_scripts/run_benchmark_test.sh b/src/tasks/denoising/resources_scripts/run_benchmark_test.sh index 7f3ecbd3d2..c9023c26f1 100755 --- a/src/tasks/denoising/resources_scripts/run_benchmark_test.sh +++ b/src/tasks/denoising/resources_scripts/run_benchmark_test.sh @@ -13,7 +13,7 @@ process { } HERE -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ +tw launch https://github.com/openproblems-bio/openproblems.git \ --revision main_build \ --pull-latest \ --main-script target/nextflow/denoising/workflows/run_benchmark/main.nf \ diff --git a/src/tasks/dimensionality_reduction/README.md b/src/tasks/dimensionality_reduction/README.md index c18c5dc5ba..c5bc42e09d 100644 --- a/src/tasks/dimensionality_reduction/README.md +++ b/src/tasks/dimensionality_reduction/README.md @@ -5,7 +5,7 @@ Reduction of high-dimensional datasets to 2D for visualization & interpretation Path: -[`src/tasks/dimensionality_reduction`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/tasks/dimensionality_reduction) +[`src/tasks/dimensionality_reduction`](https://github.com/openproblems-bio/openproblems/tree/main/src/tasks/dimensionality_reduction) ## Motivation @@ -170,7 +170,7 @@ Slot description: ## Component type: Data processor Path: -[`src/dimensionality_reduction`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/dimensionality_reduction) +[`src/dimensionality_reduction`](https://github.com/openproblems-bio/openproblems/tree/main/src/dimensionality_reduction) A dimensionality reduction dataset processor. @@ -261,7 +261,7 @@ Slot description: ## Component type: Control method Path: -[`src/dimensionality_reduction/control_methods`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/dimensionality_reduction/control_methods) +[`src/dimensionality_reduction/control_methods`](https://github.com/openproblems-bio/openproblems/tree/main/src/dimensionality_reduction/control_methods) Quality control methods for verifying the pipeline. @@ -280,7 +280,7 @@ Arguments: ## Component type: Method Path: -[`src/dimensionality_reduction/methods`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/dimensionality_reduction/methods) +[`src/dimensionality_reduction/methods`](https://github.com/openproblems-bio/openproblems/tree/main/src/dimensionality_reduction/methods) A dimensionality reduction method. @@ -298,7 +298,7 @@ Arguments: ## Component type: Metric Path: -[`src/dimensionality_reduction/metrics`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/dimensionality_reduction/metrics) +[`src/dimensionality_reduction/metrics`](https://github.com/openproblems-bio/openproblems/tree/main/src/dimensionality_reduction/metrics) A dimensionality reduction metric. diff --git a/src/tasks/dimensionality_reduction/resources_scripts/process_datasets.sh b/src/tasks/dimensionality_reduction/resources_scripts/process_datasets.sh index f83056dad6..11e911edac 100755 --- a/src/tasks/dimensionality_reduction/resources_scripts/process_datasets.sh +++ b/src/tasks/dimensionality_reduction/resources_scripts/process_datasets.sh @@ -22,7 +22,7 @@ process { } HERE -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ +tw launch https://github.com/openproblems-bio/openproblems.git \ --revision main_build \ --pull-latest \ --main-script target/nextflow/dimensionality_reduction/workflows/process_datasets/main.nf \ diff --git a/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark.sh b/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark.sh index 02c58d5cc5..5cf975d3b5 100755 --- a/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark.sh +++ b/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark.sh @@ -10,7 +10,7 @@ output_state: "state.yaml" publish_dir: "$publish_dir" HERE -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ +tw launch https://github.com/openproblems-bio/openproblems.git \ --revision main_build \ --pull-latest \ --main-script target/nextflow/dimensionality_reduction/workflows/run_benchmark/main.nf \ diff --git a/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark_test.sh b/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark_test.sh index 1c778d345c..be6defda0f 100755 --- a/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark_test.sh +++ b/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark_test.sh @@ -13,7 +13,7 @@ process { } HERE -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ +tw launch https://github.com/openproblems-bio/openproblems.git \ --revision main_build \ --pull-latest \ --main-script target/nextflow/dimensionality_reduction/workflows/run_benchmark/main.nf \ diff --git a/src/tasks/label_projection/README.md b/src/tasks/label_projection/README.md index 8981c503be..7694bc0aa6 100644 --- a/src/tasks/label_projection/README.md +++ b/src/tasks/label_projection/README.md @@ -4,7 +4,7 @@ Automated cell type annotation from rich, labeled reference data Path: -[`src/tasks/label_projection`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/tasks/label_projection) +[`src/tasks/label_projection`](https://github.com/openproblems-bio/openproblems/tree/main/src/tasks/label_projection) ## Motivation @@ -119,7 +119,7 @@ Slot description: ## Component type: Data processor Path: -[`src/label_projection`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/label_projection) +[`src/label_projection`](https://github.com/openproblems-bio/openproblems/tree/main/src/label_projection) A label projection dataset processor. @@ -255,7 +255,7 @@ Slot description: ## Component type: Control method Path: -[`src/label_projection/control_methods`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/label_projection/control_methods) +[`src/label_projection/control_methods`](https://github.com/openproblems-bio/openproblems/tree/main/src/label_projection/control_methods) Quality control methods for verifying the pipeline. @@ -275,7 +275,7 @@ Arguments: ## Component type: Method Path: -[`src/label_projection/methods`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/label_projection/methods) +[`src/label_projection/methods`](https://github.com/openproblems-bio/openproblems/tree/main/src/label_projection/methods) A label projection method. @@ -294,7 +294,7 @@ Arguments: ## Component type: Metric Path: -[`src/label_projection/metrics`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/label_projection/metrics) +[`src/label_projection/metrics`](https://github.com/openproblems-bio/openproblems/tree/main/src/label_projection/metrics) A label projection metric. diff --git a/src/tasks/label_projection/resources_scripts/process_datasets.sh b/src/tasks/label_projection/resources_scripts/process_datasets.sh index dbd284d237..d5c6353ff5 100755 --- a/src/tasks/label_projection/resources_scripts/process_datasets.sh +++ b/src/tasks/label_projection/resources_scripts/process_datasets.sh @@ -22,7 +22,7 @@ process { } HERE -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ +tw launch https://github.com/openproblems-bio/openproblems.git \ --revision main_build \ --pull-latest \ --main-script target/nextflow/label_projection/workflows/process_datasets/main.nf \ diff --git a/src/tasks/label_projection/resources_scripts/run_benchmark.sh b/src/tasks/label_projection/resources_scripts/run_benchmark.sh index 58a16c38d3..8733e22f52 100755 --- a/src/tasks/label_projection/resources_scripts/run_benchmark.sh +++ b/src/tasks/label_projection/resources_scripts/run_benchmark.sh @@ -11,7 +11,7 @@ settings: '{"method_ids": "scanvi_scarches"}' publish_dir: "$publish_dir" HERE -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ +tw launch https://github.com/openproblems-bio/openproblems.git \ --revision main_build \ --pull-latest \ --main-script target/nextflow/label_projection/workflows/run_benchmark/main.nf \ diff --git a/src/tasks/label_projection/resources_scripts/run_benchmark_test.sh b/src/tasks/label_projection/resources_scripts/run_benchmark_test.sh index 5baf56f4e4..caf699a384 100755 --- a/src/tasks/label_projection/resources_scripts/run_benchmark_test.sh +++ b/src/tasks/label_projection/resources_scripts/run_benchmark_test.sh @@ -13,7 +13,7 @@ process { } HERE -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ +tw launch https://github.com/openproblems-bio/openproblems.git \ --revision main_build \ --pull-latest \ --main-script target/nextflow/label_projection/workflows/run_benchmark/main.nf \ diff --git a/src/tasks/match_modalities/README.md b/src/tasks/match_modalities/README.md index 399c31ee92..777f367507 100644 --- a/src/tasks/match_modalities/README.md +++ b/src/tasks/match_modalities/README.md @@ -5,7 +5,7 @@ Match cells across datasets of the same set of samples on different technologies / modalities. Path: -[`src/tasks/match_modalities`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/tasks/match_modalities) +[`src/tasks/match_modalities`](https://github.com/openproblems-bio/openproblems/tree/main/src/tasks/match_modalities) ## Motivation @@ -135,7 +135,7 @@ Slot description: ## Component type: Data processor Path: -[`src/match_modalities`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/match_modalities) +[`src/match_modalities`](https://github.com/openproblems-bio/openproblems/tree/main/src/match_modalities) A match modalities dataset processor. @@ -303,7 +303,7 @@ Slot description: ## Component type: Control method Path: -[`src/match_modalities/control_methods`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/match_modalities/control_methods) +[`src/match_modalities/control_methods`](https://github.com/openproblems-bio/openproblems/tree/main/src/match_modalities/control_methods) A multimodal data integration control method. @@ -325,7 +325,7 @@ Arguments: ## Component type: Method Path: -[`src/match_modalities/methods`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/match_modalities/methods) +[`src/match_modalities/methods`](https://github.com/openproblems-bio/openproblems/tree/main/src/match_modalities/methods) A multimodal data integration method. @@ -345,7 +345,7 @@ Arguments: ## Component type: Metric Path: -[`src/match_modalities/metrics`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/match_modalities/metrics) +[`src/match_modalities/metrics`](https://github.com/openproblems-bio/openproblems/tree/main/src/match_modalities/metrics) A multimodal data integration metric. diff --git a/src/tasks/match_modalities/resources_scripts/process_datasets.sh b/src/tasks/match_modalities/resources_scripts/process_datasets.sh index 149130d0cf..e5796bd641 100755 --- a/src/tasks/match_modalities/resources_scripts/process_datasets.sh +++ b/src/tasks/match_modalities/resources_scripts/process_datasets.sh @@ -22,7 +22,7 @@ process { } HERE -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ +tw launch https://github.com/openproblems-bio/openproblems.git \ --revision main_build \ --pull-latest \ --main-script target/nextflow/match_modalities/workflows/process_datasets/main.nf \ diff --git a/src/tasks/match_modalities/resources_scripts/run_benchmark.sh b/src/tasks/match_modalities/resources_scripts/run_benchmark.sh index 001ba3437b..41789c6a0f 100755 --- a/src/tasks/match_modalities/resources_scripts/run_benchmark.sh +++ b/src/tasks/match_modalities/resources_scripts/run_benchmark.sh @@ -11,7 +11,7 @@ output_state: "state.yaml" publish_dir: "$publish_dir" HERE -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ +tw launch https://github.com/openproblems-bio/openproblems.git \ --revision main_build \ --pull-latest \ --main-script target/nextflow/match_modalities/workflows/run_benchmark/main.nf \ diff --git a/src/tasks/predict_modality/README.md b/src/tasks/predict_modality/README.md index add96684ce..4b361c52fb 100644 --- a/src/tasks/predict_modality/README.md +++ b/src/tasks/predict_modality/README.md @@ -5,7 +5,7 @@ Predicting the profiles of one modality (e.g. protein abundance) from another (e.g. mRNA expression). Path: -[`src/tasks/predict_modality`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/tasks/predict_modality) +[`src/tasks/predict_modality`](https://github.com/openproblems-bio/openproblems/tree/main/src/tasks/predict_modality) ## Motivation @@ -131,7 +131,7 @@ Slot description: ## Component type: Data processor Path: -[`src/predict_modality`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/predict_modality) +[`src/predict_modality`](https://github.com/openproblems-bio/openproblems/tree/main/src/predict_modality) A predict modality dataset processor. @@ -323,7 +323,7 @@ Slot description: ## Component type: Control method Path: -[`src/predict_modality/control_methods`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/predict_modality/control_methods) +[`src/predict_modality/control_methods`](https://github.com/openproblems-bio/openproblems/tree/main/src/predict_modality/control_methods) Quality control methods for verifying the pipeline. @@ -344,7 +344,7 @@ Arguments: ## Component type: Method Path: -[`src/predict_modality/methods`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/predict_modality/methods) +[`src/predict_modality/methods`](https://github.com/openproblems-bio/openproblems/tree/main/src/predict_modality/methods) A regression method. @@ -364,7 +364,7 @@ Arguments: ## Component type: Metric Path: -[`src/predict_modality/metrics`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/predict_modality/metrics) +[`src/predict_modality/metrics`](https://github.com/openproblems-bio/openproblems/tree/main/src/predict_modality/metrics) A predict modality metric. diff --git a/src/tasks/predict_modality/methods/lmds_irlba_rf/config.vsh.yaml b/src/tasks/predict_modality/methods/lmds_irlba_rf/config.vsh.yaml index ba86f0631e..0ed08b89aa 100644 --- a/src/tasks/predict_modality/methods/lmds_irlba_rf/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/lmds_irlba_rf/config.vsh.yaml @@ -7,8 +7,8 @@ functionality: description: | A random forest regression using LMDS of modality 1 to predict a PCA embedding of modality 2, which is then reversed to predict the original modality 2. reference: lance2022multimodal - documentation_url: https://github.com/openproblems-bio/openproblems-v2/tree/main/src/tasks/predict_modality/methods #/lmds_irlba_rf - repository_url: https://github.com/openproblems-bio/openproblems-v2 + documentation_url: https://github.com/openproblems-bio/openproblems/tree/main/src/tasks/predict_modality/methods #/lmds_irlba_rf + repository_url: https://github.com/openproblems-bio/openproblems preferred_normalization: log_cp10k arguments: - name: "--distance_method" diff --git a/src/tasks/predict_modality/resources_scripts/process_datasets.sh b/src/tasks/predict_modality/resources_scripts/process_datasets.sh index 69d886725f..7be4d548c1 100755 --- a/src/tasks/predict_modality/resources_scripts/process_datasets.sh +++ b/src/tasks/predict_modality/resources_scripts/process_datasets.sh @@ -10,7 +10,7 @@ output_state: "$id/state.yaml" publish_dir: s3://openproblems-data/resources/predict_modality/datasets HERE -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ +tw launch https://github.com/openproblems-bio/openproblems.git \ --revision main_build \ --pull-latest \ --main-script target/nextflow/predict_modality/workflows/process_datasets/main.nf \ diff --git a/src/tasks/predict_modality/resources_scripts/run_benchmark.sh b/src/tasks/predict_modality/resources_scripts/run_benchmark.sh index 6d4d35219c..941776be43 100755 --- a/src/tasks/predict_modality/resources_scripts/run_benchmark.sh +++ b/src/tasks/predict_modality/resources_scripts/run_benchmark.sh @@ -12,7 +12,7 @@ output_state: "state.yaml" publish_dir: "$publish_dir" HERE -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ +tw launch https://github.com/openproblems-bio/openproblems.git \ --revision main_build \ --pull-latest \ --main-script target/nextflow/predict_modality/workflows/run_benchmark/main.nf \ diff --git a/src/tasks/spatial_decomposition/README.md b/src/tasks/spatial_decomposition/README.md index 0b3cfc85d9..d5a8b58751 100644 --- a/src/tasks/spatial_decomposition/README.md +++ b/src/tasks/spatial_decomposition/README.md @@ -5,7 +5,7 @@ Estimation of cell type proportions per spot in 2D space from spatial transcriptomic data coupled with corresponding single-cell data Path: -[`src/tasks/spatial_decomposition`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/tasks/spatial_decomposition) +[`src/tasks/spatial_decomposition`](https://github.com/openproblems-bio/openproblems/tree/main/src/tasks/spatial_decomposition) ## Motivation @@ -121,7 +121,7 @@ Slot description: ## Component type: Data processor Path: -[`src/spatial_decomposition`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/spatial_decomposition) +[`src/spatial_decomposition`](https://github.com/openproblems-bio/openproblems/tree/main/src/spatial_decomposition) A spatial decomposition dataset processor. @@ -239,7 +239,7 @@ Slot description: ## Component type: Control method Path: -[`src/spatial_decomposition/control_methods`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/spatial_decomposition/control_methods) +[`src/spatial_decomposition/control_methods`](https://github.com/openproblems-bio/openproblems/tree/main/src/spatial_decomposition/control_methods) Quality control methods for verifying the pipeline. @@ -259,7 +259,7 @@ Arguments: ## Component type: Method Path: -[`src/spatial_decomposition/methods`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/spatial_decomposition/methods) +[`src/spatial_decomposition/methods`](https://github.com/openproblems-bio/openproblems/tree/main/src/spatial_decomposition/methods) A spatial composition method. @@ -278,7 +278,7 @@ Arguments: ## Component type: Metric Path: -[`src/spatial_decomposition/metrics`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/spatial_decomposition/metrics) +[`src/spatial_decomposition/metrics`](https://github.com/openproblems-bio/openproblems/tree/main/src/spatial_decomposition/metrics) A spatial decomposition metric. diff --git a/src/tasks/spatial_decomposition/resources_scripts/process_datasets.sh b/src/tasks/spatial_decomposition/resources_scripts/process_datasets.sh index 337aa34512..39ea9604e3 100755 --- a/src/tasks/spatial_decomposition/resources_scripts/process_datasets.sh +++ b/src/tasks/spatial_decomposition/resources_scripts/process_datasets.sh @@ -24,7 +24,7 @@ process { } HERE -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ +tw launch https://github.com/openproblems-bio/openproblems.git \ --revision main_build \ --pull-latest \ --main-script target/nextflow/spatial_decomposition/workflows/process_datasets/main.nf \ diff --git a/src/tasks/spatial_decomposition/resources_scripts/run_benchmark.sh b/src/tasks/spatial_decomposition/resources_scripts/run_benchmark.sh index 85d5e4fb1e..db22b76f3a 100755 --- a/src/tasks/spatial_decomposition/resources_scripts/run_benchmark.sh +++ b/src/tasks/spatial_decomposition/resources_scripts/run_benchmark.sh @@ -10,7 +10,7 @@ output_state: "state.yaml" publish_dir: "$publish_dir" HERE -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ +tw launch https://github.com/openproblems-bio/openproblems.git \ --revision main_build \ --pull-latest \ --main-script target/nextflow/spatial_decomposition/workflows/run_benchmark/main.nf \ diff --git a/src/tasks/spatially_variable_genes/README.md b/src/tasks/spatially_variable_genes/README.md index 315c01900a..5e9f43407d 100644 --- a/src/tasks/spatially_variable_genes/README.md +++ b/src/tasks/spatially_variable_genes/README.md @@ -11,7 +11,7 @@ significantly across different spatial regions within a tissue or across cells in a spatially structured context. Path to source: -[`src/tasks/spatially_variable_genes`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/tasks/spatially_variable_genes) +[`src/tasks/spatially_variable_genes`](https://github.com/openproblems-bio/openproblems/tree/main/src/tasks/spatially_variable_genes) ## Motivation @@ -121,7 +121,7 @@ Slot description: ## Component type: Data processor Path: -[`src/spatially_variable_genes`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/spatially_variable_genes) +[`src/spatially_variable_genes`](https://github.com/openproblems-bio/openproblems/tree/main/src/spatially_variable_genes) A spatially variable genes dataset processor. @@ -216,7 +216,7 @@ Slot description: ## Component type: Control method Path: -[`src/spatially_variable_genes/control_methods`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/spatially_variable_genes/control_methods) +[`src/spatially_variable_genes/control_methods`](https://github.com/openproblems-bio/openproblems/tree/main/src/spatially_variable_genes/control_methods) Quality control methods for verifying the pipeline. @@ -235,7 +235,7 @@ Arguments: ## Component type: Method Path: -[`src/spatially_variable_genes/methods`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/spatially_variable_genes/methods) +[`src/spatially_variable_genes/methods`](https://github.com/openproblems-bio/openproblems/tree/main/src/spatially_variable_genes/methods) A spatially variable gene identification method. @@ -253,7 +253,7 @@ Arguments: ## Component type: Metric Path: -[`src/spatially_variable_genes/metrics`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/spatially_variable_genes/metrics) +[`src/spatially_variable_genes/metrics`](https://github.com/openproblems-bio/openproblems/tree/main/src/spatially_variable_genes/metrics) A spatially variable genes identification metric. diff --git a/src/tasks/spatially_variable_genes/resources_scripts/process_datasets.sh b/src/tasks/spatially_variable_genes/resources_scripts/process_datasets.sh index bdd90f9786..74b18f465c 100755 --- a/src/tasks/spatially_variable_genes/resources_scripts/process_datasets.sh +++ b/src/tasks/spatially_variable_genes/resources_scripts/process_datasets.sh @@ -99,7 +99,7 @@ process { } HERE -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ +tw launch https://github.com/openproblems-bio/openproblems.git \ --revision integration_build \ --pull-latest \ --main-script target/nextflow/spatially_variable_genes/workflows/process_datasets/main.nf \ diff --git a/src/tasks/spatially_variable_genes/resources_scripts/run_benchmark.sh b/src/tasks/spatially_variable_genes/resources_scripts/run_benchmark.sh index 9539cea4fe..8620bbafe8 100755 --- a/src/tasks/spatially_variable_genes/resources_scripts/run_benchmark.sh +++ b/src/tasks/spatially_variable_genes/resources_scripts/run_benchmark.sh @@ -53,7 +53,7 @@ output_state: "state.yaml" publish_dir: "$publish_dir" HERE -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ +tw launch https://github.com/openproblems-bio/openproblems.git \ --revision integration_build \ --pull-latest \ --main-script target/nextflow/spatially_variable_genes/workflows/run_benchmark/main.nf \