diff --git a/src/control_methods/random_proportions/config.vsh.yaml b/src/control_methods/random_proportions/config.vsh.yaml index 6cd801b..acffb79 100644 --- a/src/control_methods/random_proportions/config.vsh.yaml +++ b/src/control_methods/random_proportions/config.vsh.yaml @@ -1,11 +1,11 @@ __merge__: ../../api/comp_control_method.yaml name: random_proportions +label: Random Proportions +summary: "Negative control method that randomly assigns celltype proportions from a Dirichlet distribution." +description: | + A negative control method with random assignment of predicted celltype proportions from a Dirichlet distribution. info: - label: Random Proportions - summary: "Negative control method that randomly assigns celltype proportions from a Dirichlet distribution." - description: | - A negative control method with random assignment of predicted celltype proportions from a Dirichlet distribution. preferred_normalization: counts resources: @@ -14,7 +14,7 @@ resources: engines: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: numpy diff --git a/src/control_methods/true_proportions/config.vsh.yaml b/src/control_methods/true_proportions/config.vsh.yaml index b3d980f..7cae84d 100644 --- a/src/control_methods/true_proportions/config.vsh.yaml +++ b/src/control_methods/true_proportions/config.vsh.yaml @@ -14,7 +14,7 @@ resources: engines: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 runners: - type: executable diff --git a/src/methods/cell2location/config.vsh.yaml b/src/methods/cell2location/config.vsh.yaml index bbcd662..be96c02 100644 --- a/src/methods/cell2location/config.vsh.yaml +++ b/src/methods/cell2location/config.vsh.yaml @@ -70,7 +70,7 @@ resources: engines: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: diff --git a/src/methods/destvi/config.vsh.yaml b/src/methods/destvi/config.vsh.yaml index a5b9b62..e27d8a9 100644 --- a/src/methods/destvi/config.vsh.yaml +++ b/src/methods/destvi/config.vsh.yaml @@ -27,7 +27,7 @@ resources: engines: - type: docker - image: ghcr.io/openproblems-bio/base_pytorch_nvidia:1.0.4 + image: openproblems/base_pytorch_nvidia:1.0.0 setup: - type: python packages: diff --git a/src/methods/nmfreg/config.vsh.yaml b/src/methods/nmfreg/config.vsh.yaml index c2ba51c..3533f08 100644 --- a/src/methods/nmfreg/config.vsh.yaml +++ b/src/methods/nmfreg/config.vsh.yaml @@ -23,7 +23,7 @@ resources: engines: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: diff --git a/src/methods/nnls/config.vsh.yaml b/src/methods/nnls/config.vsh.yaml index 9dd1a2d..a9af655 100644 --- a/src/methods/nnls/config.vsh.yaml +++ b/src/methods/nnls/config.vsh.yaml @@ -17,7 +17,7 @@ resources: engines: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: diff --git a/src/methods/rctd/config.vsh.yaml b/src/methods/rctd/config.vsh.yaml index d97e16b..321e061 100644 --- a/src/methods/rctd/config.vsh.yaml +++ b/src/methods/rctd/config.vsh.yaml @@ -27,7 +27,7 @@ resources: engines: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.4 + image: openproblems/base_r:1.0.0 setup: - type: r cran: [ Matrix, pak ] diff --git a/src/methods/seurat/config.vsh.yaml b/src/methods/seurat/config.vsh.yaml index 3fcd2c6..9c63222 100644 --- a/src/methods/seurat/config.vsh.yaml +++ b/src/methods/seurat/config.vsh.yaml @@ -27,7 +27,7 @@ resources: engines: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.4 + image: openproblems/base_r:1.0.0 setup: - type: r cran: [Matrix, Seurat] diff --git a/src/methods/stereoscope/config.vsh.yaml b/src/methods/stereoscope/config.vsh.yaml index 99fa90f..2ffaa11 100644 --- a/src/methods/stereoscope/config.vsh.yaml +++ b/src/methods/stereoscope/config.vsh.yaml @@ -28,7 +28,7 @@ resources: engines: - type: docker - image: ghcr.io/openproblems-bio/base_pytorch_nvidia:1.0.4 + image: openproblems/base_pytorch_nvidia:1.0.0 setup: - type: python packages: diff --git a/src/methods/tangram/config.vsh.yaml b/src/methods/tangram/config.vsh.yaml index a004bf8..0bb5aeb 100644 --- a/src/methods/tangram/config.vsh.yaml +++ b/src/methods/tangram/config.vsh.yaml @@ -27,7 +27,7 @@ resources: engines: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: tangram-sc diff --git a/src/methods/vanillanmf/config.vsh.yaml b/src/methods/vanillanmf/config.vsh.yaml index a7d8ba5..232e816 100644 --- a/src/methods/vanillanmf/config.vsh.yaml +++ b/src/methods/vanillanmf/config.vsh.yaml @@ -23,7 +23,7 @@ resources: engines: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: diff --git a/src/metrics/jsd/config.vsh.yaml b/src/metrics/jsd/config.vsh.yaml index abe5a67..62e6bc6 100644 --- a/src/metrics/jsd/config.vsh.yaml +++ b/src/metrics/jsd/config.vsh.yaml @@ -21,7 +21,7 @@ resources: engines: - type: docker - image: ghcr.io/openproblems-bio/base_images/python:1.1.0 + image: openproblems/base_python:1.0.0 setup: - type: python packages: [numpy, scipy] diff --git a/src/metrics/r2/config.vsh.yaml b/src/metrics/r2/config.vsh.yaml index 631f0aa..30ba527 100644 --- a/src/metrics/r2/config.vsh.yaml +++ b/src/metrics/r2/config.vsh.yaml @@ -21,7 +21,7 @@ resources: engines: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: openproblems/base_python:1.0.0 setup: - type: python packages: scikit-learn diff --git a/src/workflows/process_datasets/config.vsh.yaml b/src/workflows/process_datasets/config.vsh.yaml index ce30fd2..1fac1cd 100644 --- a/src/workflows/process_datasets/config.vsh.yaml +++ b/src/workflows/process_datasets/config.vsh.yaml @@ -1,5 +1,5 @@ -namespace: "workflows" -name: "process_datasets" +namespace: workflows +name: process_datasets argument_groups: - name: Inputs arguments: diff --git a/src/workflows/run_benchmark/config.vsh.yaml b/src/workflows/run_benchmark/config.vsh.yaml index fe39aa1..cfa3a32 100644 --- a/src/workflows/run_benchmark/config.vsh.yaml +++ b/src/workflows/run_benchmark/config.vsh.yaml @@ -1,5 +1,5 @@ -name: "run_benchmark" -namespace: "workflows" +name: run_benchmark +namespace: workflows argument_groups: - name: Inputs arguments: @@ -47,8 +47,6 @@ resources: - type: nextflow_script path: main.nf entrypoint: run_wf - - type: file - path: "../../api/task_info.yaml" dependencies: - name: common/check_dataset_schema repository: openproblems_v2