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Merged
merged 3 commits into from
May 22, 2025
Merged

Update scripts #57

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b8a4c7f
Fix scripts
rcannood May 15, 2025
e7efcb2
update common
rcannood May 15, 2025
12c1fac
Merge branch 'main' into fix-scripts
ghar1821 May 22, 2025
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2 changes: 1 addition & 1 deletion common
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Submodule common updated 11 files
+4 −4 component_tests/run_and_check_output.py
+21 −0 nextflow_helpers/README.md
+232 −0 nextflow_helpers/benchmarkHelper.nf
+17 −0 nextflow_helpers/helper.nf
+53 −8 nextflow_helpers/labels_tw.config
+2,786 −0 nextflow_helpers/workflowHelper.nf
+15 −3 scripts/create_component
+16 −4 scripts/create_task_readme
+40 −0 scripts/fetch_task_run
+15 −3 scripts/sync_resources
+13 −1 scripts/upgrade_config
15 changes: 1 addition & 14 deletions scripts/run_benchmark/run_full_local.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -6,19 +6,6 @@ REPO_ROOT=$(git rev-parse --show-toplevel)
# ensure that the command below is run from the root of the repository
cd "$REPO_ROOT"

# NOTE: depending on the the datasets and components, you may need to launch this workflow
# on a different compute platform (e.g. a HPC, AWS Cloud, Azure Cloud, Google Cloud).
# please refer to the nextflow information for more details:
# https://www.nextflow.io/docs/latest/

# remove this when you have implemented the script
echo "TODO: once the 'run_benchmark' workflow has been implemented, update this script to use it."
echo " Step 1: replace 'task_cyto_batch_integration' with the name of the task in the following command."
echo " Step 2: replace the rename keys parameters to fit your run_benchmark inputs"
echo " Step 3: replace the settings parameter to fit your run_benchmark outputs"
echo " Step 4: remove this message"
exit 1

set -e

echo "Running benchmark on test data"
Expand All @@ -31,7 +18,7 @@ publish_dir="resources/results/${RUN_ID}"
# write the parameters to file
cat > /tmp/params.yaml << HERE
input_states: resources/datasets/**/state.yaml
rename_keys: 'input_train:output_train;input_test:output_test;input_solution:output_solution'
rename_keys: 'input_unintegrated_censored:output_unintegrated_censored;input_unintegrated:output_unintegrated;input_validation:output_validation'
output_state: "state.yaml"
publish_dir: "$publish_dir"
HERE
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2 changes: 1 addition & 1 deletion scripts/run_benchmark/run_full_seqeracloud.sh
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Expand Up @@ -15,7 +15,7 @@ publish_dir="s3://openproblems-data/resources/task_cyto_batch_integration/result
# write the parameters to file
cat > /tmp/params.yaml << HERE
input_states: s3://openproblems-data/resources/task_cyto_batch_integration/datasets/**/state.yaml
rename_keys: 'input_unintegrated_censored:unintegrated_censored;input_unintegrated:unintegrated;input_validation:validation'
rename_keys: 'input_unintegrated_censored:output_unintegrated_censored;input_unintegrated:output_unintegrated;input_validation:output_validation'
output_state: "state.yaml"
publish_dir: "$publish_dir"
HERE
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