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Add denbi config and script #21

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Merged
rcannood merged 1 commit into from
Jul 29, 2026
+33 −1
Merged

Add denbi config and script #21

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2 changes: 1 addition & 1 deletion common
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Submodule common updated 21 files
+7 −160 component_tests/check_config.py
+6 −174 component_tests/run_and_check_output.py
+21 −0 nextflow_helpers/README.md
+232 −0 nextflow_helpers/benchmarkHelper.nf
+88 −0 nextflow_helpers/labels_denbi.config
+58 −9 nextflow_helpers/labels_tw.config
+2,786 −0 nextflow_helpers/workflowHelper.nf
+64 −0 schemas/results_v4/core.json
+91 −0 schemas/results_v4/dataset_info.json
+85 −0 schemas/results_v4/method_info.json
+78 −0 schemas/results_v4/metric_info.json
+51 −0 schemas/results_v4/quality_control.json
+184 −0 schemas/results_v4/results.json
+71 −0 schemas/results_v4/task_info.json
+36 −0 schemas/results_v4/task_results.json
+3 −3 scripts/create_component
+4 −4 scripts/create_task_readme
+4 −4 scripts/fetch_task_run
+465 −0 scripts/render_results_report
+3 −3 scripts/sync_resources
+1 −1 scripts/upgrade_config
32 changes: 32 additions & 0 deletions scripts/run_benchmark/run_full_denbi.sh
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Original file line number Diff line number Diff line change
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#!/bin/bash

# get the root of the directory
REPO_ROOT=$(git rev-parse --show-toplevel)

# ensure that the command below is run from the root of the repository
cd "$REPO_ROOT"

set -e

# generate a unique id
RUN_ID="run_$(date +%Y-%m-%d_%H-%M-%S)"
publish_dir="/vol/scratch/results/task_predict_modality/${RUN_ID}"

# 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"
output_state: "state.yaml"
publish_dir: "$publish_dir"
HERE

tw launch https://github.com/openproblems-bio/task_predict_modality.git \
--revision build/main \
--pull-latest \
--main-script target/nextflow/workflows/run_benchmark/main.nf \
--workspace 53907369739130 \
--compute-env 3qstFmP9lNwdzutSNuJq7c \
--params-file /tmp/params.yaml \
--entry-name auto \
--config common/nextflow_helpers/labels_denbi.config \
--labels task_predict_modality,full,denbi
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