diff --git a/_viash.yaml b/_viash.yaml index 4576802..226469c 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -86,16 +86,10 @@ info: dest: resources_test/task_predict_modality repositories: - - name: openproblems_v2 + - name: openproblems type: github - repo: openproblems-bio/openproblems-v2 + repo: openproblems-bio/openproblems tag: main_build - - name: core - type: github - repo: openproblems-bio/core - # tag: build/main - tag: build/add_common_components - path: viash/core 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" } diff --git a/common b/common index f264283..65e05af 160000 --- a/common +++ b/common @@ -1 +1 @@ -Subproject commit f2642835c89264e0a43e87e3f6c588c6be4902e7 +Subproject commit 65e05af68a11ee87853fcf7a3c6b579001f21abe diff --git a/scripts/create_datasets/resources.sh b/scripts/create_datasets/resources.sh index 004d90f..94ecda7 100755 --- a/scripts/create_datasets/resources.sh +++ b/scripts/create_datasets/resources.sh @@ -19,7 +19,7 @@ tw launch https://github.com/openproblems-bio/task_predict_modality.git \ --pull-latest \ --main-script target/nextflow/workflows/process_datasets/main.nf \ --workspace 53907369739130 \ - --compute-env 6TeIFgV5OY4pJCk8I0bfOh \ + --compute-env 5DwwhQoBi0knMSGcwThnlF \ --params-file /tmp/params.yaml \ --entry-name auto \ --config common/nextflow_helpers/labels_tw.config \ diff --git a/scripts/run_benchmark/run_full_seqeracloud.sh b/scripts/run_benchmark/run_full_seqeracloud.sh index f7ad1ef..fab22bd 100755 --- a/scripts/run_benchmark/run_full_seqeracloud.sh +++ b/scripts/run_benchmark/run_full_seqeracloud.sh @@ -14,8 +14,8 @@ publish_dir="s3://openproblems-data/resources/task_predict_modality/results/${RU # write the parameters to file cat > /tmp/params.yaml << HERE -input_states: s3://openproblems-data/resources/task_predict_modality/datasets/**/state.yaml -rename_keys: 'input_train_mod1:output_train_mod1;input_train_mod2:output_train_mod2;input_test_mod1:output_test_mod1;input_test_mod2:output_test_mod2" +input_states: "s3://openproblems-data/resources/task_predict_modality/datasets/**/state.yaml" +rename_keys: "input_train_mod1:output_train_mod1;input_train_mod2:output_train_mod2;input_test_mod1:output_test_mod1;input_test_mod2:output_test_mod2" output_state: "state.yaml" publish_dir: "$publish_dir" HERE @@ -25,7 +25,7 @@ tw launch https://github.com/openproblems-bio/task_predict_modality.git \ --pull-latest \ --main-script target/nextflow/workflows/run_benchmark/main.nf \ --workspace 53907369739130 \ - --compute-env 6TeIFgV5OY4pJCk8I0bfOh \ + --compute-env 5DwwhQoBi0knMSGcwThnlF \ --params-file /tmp/params.yaml \ --entry-name auto \ --config common/nextflow_helpers/labels_tw.config \ diff --git a/scripts/run_benchmark/run_test_seqeracloud.sh b/scripts/run_benchmark/run_test_seqeracloud.sh index e50d8cc..9aa988a 100755 --- a/scripts/run_benchmark/run_test_seqeracloud.sh +++ b/scripts/run_benchmark/run_test_seqeracloud.sh @@ -34,7 +34,7 @@ tw launch https://github.com/openproblems-bio/task_predict_modality.git \ --pull-latest \ --main-script target/nextflow/workflows/run_benchmark/main.nf \ --workspace 53907369739130 \ - --compute-env 6TeIFgV5OY4pJCk8I0bfOh \ + --compute-env 5DwwhQoBi0knMSGcwThnlF \ --params-file /tmp/params.yaml \ --config common/nextflow_helpers/labels_tw.config \ --labels task_predict_modality,test diff --git a/src/control_methods/mean_per_gene/config.vsh.yaml b/src/control_methods/mean_per_gene/config.vsh.yaml index a18cc94..f111291 100644 --- a/src/control_methods/mean_per_gene/config.vsh.yaml +++ b/src/control_methods/mean_per_gene/config.vsh.yaml @@ -13,5 +13,5 @@ runners: - type: executable - type: nextflow directives: - label: [midtime, lowmem, lowcpu] + label: [midtime, midmem, lowcpu] \ No newline at end of file diff --git a/src/control_methods/random_predict/config.vsh.yaml b/src/control_methods/random_predict/config.vsh.yaml index 315f876..9e2bd0d 100644 --- a/src/control_methods/random_predict/config.vsh.yaml +++ b/src/control_methods/random_predict/config.vsh.yaml @@ -13,4 +13,4 @@ runners: - type: executable - type: nextflow directives: - label: [midtime, lowmem, lowcpu] + label: [midtime, midmem, lowcpu] diff --git a/src/control_methods/solution/config.vsh.yaml b/src/control_methods/solution/config.vsh.yaml index b949939..7c5fab7 100644 --- a/src/control_methods/solution/config.vsh.yaml +++ b/src/control_methods/solution/config.vsh.yaml @@ -13,4 +13,4 @@ runners: - type: executable - type: nextflow directives: - label: [midtime, lowmem, lowcpu] + label: [midtime, midmem, lowcpu] diff --git a/src/control_methods/zeros/config.vsh.yaml b/src/control_methods/zeros/config.vsh.yaml index 52e4e8d..0e1feaa 100644 --- a/src/control_methods/zeros/config.vsh.yaml +++ b/src/control_methods/zeros/config.vsh.yaml @@ -13,4 +13,4 @@ runners: - type: executable - type: nextflow directives: - label: [midtime, lowmem, lowcpu] + label: [midtime, midmem, lowcpu] diff --git a/src/methods/knnr_py/config.vsh.yaml b/src/methods/knnr_py/config.vsh.yaml index 04fa956..7a9bba6 100644 --- a/src/methods/knnr_py/config.vsh.yaml +++ b/src/methods/knnr_py/config.vsh.yaml @@ -32,4 +32,4 @@ runners: - type: executable - type: nextflow directives: - label: [hightime, lowmem, lowcpu] + label: [hightime, midmem, midcpu] diff --git a/src/methods/knnr_r/config.vsh.yaml b/src/methods/knnr_r/config.vsh.yaml index fbc5331..52cdaa5 100644 --- a/src/methods/knnr_r/config.vsh.yaml +++ b/src/methods/knnr_r/config.vsh.yaml @@ -35,4 +35,4 @@ runners: - type: executable - type: nextflow directives: - label: [hightime, lowmem, lowcpu] + label: [hightime, midmem, midcpu] diff --git a/src/workflows/process_datasets/config.vsh.yaml b/src/workflows/process_datasets/config.vsh.yaml index f4e1fee..db75632 100644 --- a/src/workflows/process_datasets/config.vsh.yaml +++ b/src/workflows/process_datasets/config.vsh.yaml @@ -7,10 +7,10 @@ resources: entrypoint: run_wf - path: /common/nextflow_helpers/helper.nf dependencies: - - name: schema/verify_data_structure - repository: core - - name: h5ad/extract_uns_metadata - repository: core + - name: validation/check_dataset_with_schema + repository: openproblems + - name: utils/extract_uns_metadata + repository: openproblems - name: data_processors/process_dataset runners: - type: nextflow diff --git a/src/workflows/process_datasets/main.nf b/src/workflows/process_datasets/main.nf index 0fff9dd..477e8cc 100644 --- a/src/workflows/process_datasets/main.nf +++ b/src/workflows/process_datasets/main.nf @@ -16,8 +16,8 @@ workflow run_wf { output_ch = input_ch // Check if the input datasets match the desired format -------------------------------- - | verify_data_structure.run( - key: "verify_data_structure_mod1", + | check_dataset_with_schema.run( + key: "check_dataset_with_schema_mod1", fromState: { id, state -> def schema = findArgumentSchema(meta.config, "input_mod1") def schemaYaml = tempFile("schema.yaml") @@ -36,8 +36,8 @@ workflow run_wf { } ) - | verify_data_structure.run( - key: "verify_data_structure_mod2", + | check_dataset_with_schema.run( + key: "check_dataset_with_schema_mod2", fromState: { id, state -> def schema = findArgumentSchema(meta.config, "input_mod2") def schemaYaml = tempFile("schema.yaml") diff --git a/src/workflows/run_benchmark/config.vsh.yaml b/src/workflows/run_benchmark/config.vsh.yaml index 77be6bd..65f222e 100644 --- a/src/workflows/run_benchmark/config.vsh.yaml +++ b/src/workflows/run_benchmark/config.vsh.yaml @@ -60,8 +60,8 @@ resources: - type: file path: /_viash.yaml dependencies: - - name: h5ad/extract_uns_metadata - repository: core + - name: utils/extract_uns_metadata + repository: openproblems - name: control_methods/mean_per_gene - name: control_methods/random_predict - name: control_methods/zeros