diff --git a/_viash.yaml b/_viash.yaml index 94d2ade4..8776016d 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -1,4 +1,4 @@ -viash_version: 0.9.0 +viash_version: 0.9.4 name: task_spatial_simulators organization: openproblems-bio @@ -64,7 +64,7 @@ links: docker_registry: ghcr.io info: - # image: thumbnail.svg + image: thumbnail.svg test_resources: - type: s3 @@ -79,4 +79,4 @@ repositories: 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" } - .runners[.type == "nextflow"].config.script := "process.errorStrategy = 'ignore'" \ No newline at end of file + .runners[.type == "nextflow"].config.script := "process.errorStrategy = 'ignore'" diff --git a/src/api/comp_process_datasets.yaml b/src/api/comp_process_datasets.yaml index 23c9a935..0860ddca 100644 --- a/src/api/comp_process_datasets.yaml +++ b/src/api/comp_process_datasets.yaml @@ -53,11 +53,11 @@ argument_groups: test_default: MOBNEW - type: string name: --dataset_url_spatial - description: Link to the original source of the dataset. + description: Link to the original source of the spatial dataset. required: false - type: string name: --dataset_url_singlecell - description: Link to the original source of the dataset. + description: Link to the original source of the single-cell dataset. required: false - type: string name: --dataset_reference @@ -66,35 +66,35 @@ argument_groups: required: false - type: string name: --dataset_reference_spatial - description: A doi for the dataset. + description: A doi for the spatial dataset. example: 10.1234/s1234-5678-9012-3 required: false - type: string name: --dataset_reference_singlecell - description: A doi for the dataset. + description: A doi for the single-cell dataset. example: 10.1234/s1234-5678-9012-3 required: false - type: string name: --dataset_summary_spatial - description: Short description of the dataset. + description: Short description of the spatial dataset. required: true info: test_default: MOBNEW - type: string name: --dataset_summary_singlecell - description: Short description of the dataset. + description: Short description of the single-cell dataset. required: true info: test_default: MOBNEW - type: string name: --dataset_description_spatial - description: Long description of the dataset. + description: Long description of the spatial dataset. required: true info: test_default: MOBNEW - type: string name: --dataset_description_singlecell - description: Long description of the dataset. + description: Long description of the single-cell dataset. required: true info: test_default: MOBNEW diff --git a/src/workflows/run_benchmark/config.vsh.yaml b/src/workflows/run_benchmark/config.vsh.yaml index 2da5876e..5741108e 100644 --- a/src/workflows/run_benchmark/config.vsh.yaml +++ b/src/workflows/run_benchmark/config.vsh.yaml @@ -64,4 +64,4 @@ dependencies: - name: metrics/ks_statistic_sc_features - name: process_datasets/generate_sim_spatialcluster runners: - - type: nextflow \ No newline at end of file + - type: nextflow diff --git a/src/workflows/run_benchmark/main.nf b/src/workflows/run_benchmark/main.nf index 295722b7..b345edab 100644 --- a/src/workflows/run_benchmark/main.nf +++ b/src/workflows/run_benchmark/main.nf @@ -24,8 +24,7 @@ methods = [ metrics = [ downstream, ks_statistic_gene_cell, - ks_statistic_sc_features, - ks_statistic_spatial + ks_statistic_sc_features ] workflow run_wf {