diff --git a/CHANGELOG.md b/CHANGELOG.md index 3839744..5962f06 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,6 +18,10 @@ * Updated configs, components and CI to the latest Viash version (PR #8). +* Updated to Viash 0.9.4 (PR #12). + +* Use dependencies in `openproblems-bio/openproblems` (PR #12). + ## MINOR CHANGES * Updated `README.md` (PR #5). diff --git a/_viash.yaml b/_viash.yaml index 83d3568..b3fa2d6 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -1,4 +1,4 @@ -viash_version: 0.9.0 +viash_version: 0.9.4 # Step 1: Change the name of the task. # example: task_name_of_this_task @@ -75,14 +75,14 @@ authors: linkedin: johndoe # Step 7: Remove all of the comments of the steps you completed -# Step 8: High five yourself! config_mods: | .runners[.type == "nextflow"].config.labels := { lowmem : "memory = 20.Gb", midmem : "memory = 50.Gb", highmem : "memory = 100.Gb", lowcpu : "cpus = 5", midcpu : "cpus = 15", highcpu : "cpus = 30", lowtime : "time = 1.h", midtime : "time = 4.h", hightime : "time = 8.h", veryhightime : "time = 24.h" } repositories: - - name: core + - name: op type: github - repo: openproblems-bio/core - tag: build/main - path: viash/core + repo: openproblems-bio/openproblems + tag: build/main # Step 8: Set this to the latest release + +# Step 9: High five yourself! diff --git a/src/workflows/process_datasets/config.vsh.yaml b/src/workflows/process_datasets/config.vsh.yaml index 64ff740..d2e4915 100644 --- a/src/workflows/process_datasets/config.vsh.yaml +++ b/src/workflows/process_datasets/config.vsh.yaml @@ -30,8 +30,8 @@ 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 25d1260..2732475 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 904a2b6..ba1e167 100644 --- a/src/workflows/run_benchmark/config.vsh.yaml +++ b/src/workflows/run_benchmark/config.vsh.yaml @@ -62,8 +62,8 @@ resources: path: /_viash.yaml dependencies: - - name: h5ad/extract_uns_metadata - repository: core + - name: utils/extract_uns_metadata + repository: op - name: control_methods/true_labels - name: methods/logistic_regression - name: metrics/accuracy