diff --git a/_viash.yaml b/_viash.yaml index 1598a22..d1be031 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -88,6 +88,5 @@ config_mods: | repositories: - name: core type: github - repo: openproblems-bio/core + repo: openproblems-bio/openproblems tag: build/main - path: viash/core diff --git a/scripts/run_benchmark/run_test_seqeracloud.sh b/scripts/run_benchmark/run_test_seqeracloud.sh index 9201487..1b1cecd 100755 --- a/scripts/run_benchmark/run_test_seqeracloud.sh +++ b/scripts/run_benchmark/run_test_seqeracloud.sh @@ -13,7 +13,7 @@ cat > /tmp/params.yaml << 'HERE' input_states: s3://openproblems-data/resources_test/task_batch_integration/**/state.yaml rename_keys: 'input_dataset:output_dataset;input_solution:output_solution' output_state: "state.yaml" -publish_dir: s3://openproblems-nextflow/temp/task_batch_integration/ +publish_dir: s3://openproblems-work/temp/task_batch_integration/ HERE tw launch https://github.com/openproblems-bio/task_batch_integration.git \ diff --git a/src/workflows/process_datasets/config.vsh.yaml b/src/workflows/process_datasets/config.vsh.yaml index 032cc8e..77a97d6 100644 --- a/src/workflows/process_datasets/config.vsh.yaml +++ b/src/workflows/process_datasets/config.vsh.yaml @@ -26,8 +26,8 @@ resources: - path: /common/nextflow_helpers/helper.nf dependencies: - - name: schema/verify_data_structure - repository: core + - name: validation/check_dataset_with_schema + repository: openproblems - name: data_processors/process_dataset runners: diff --git a/src/workflows/process_datasets/main.nf b/src/workflows/process_datasets/main.nf index 58007ad..fc2b142 100644 --- a/src/workflows/process_datasets/main.nf +++ b/src/workflows/process_datasets/main.nf @@ -14,7 +14,7 @@ workflow run_wf { main: output_ch = input_ch - | verify_data_structure.run( + | check_dataset_with_schema.run( fromState: { id, state -> def schema = findArgumentSchema(meta.config, "input") def schemaYaml = tempFile("schema.yaml") diff --git a/src/workflows/run_benchmark/config.vsh.yaml b/src/workflows/run_benchmark/config.vsh.yaml index b891a2a..1047ea8 100644 --- a/src/workflows/run_benchmark/config.vsh.yaml +++ b/src/workflows/run_benchmark/config.vsh.yaml @@ -70,8 +70,8 @@ resources: - path: /common/nextflow_helpers/helper.nf dependencies: - - name: h5ad/extract_uns_metadata - repository: core + - name: utils/extract_uns_metadata + repository: openproblems # control methods - name: control_methods/embed_cell_types - name: control_methods/embed_cell_types_jittered