fix scripts and submodule

openproblems-bio · Sep 8, 2024 · e52d07e · e52d07e
1 parent 405ea62
commit e52d07e
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Showing 3 changed files with 15 additions and 5 deletions.
diff --git a/common b/common
diff --git a/scripts/run_benchmark/run_full_local.sh b/scripts/run_benchmark/run_full_local.sh
@@ -21,6 +21,9 @@ exit 1
 
 set -e
 
+echo "Running benchmark on test data"
+echo "  Make sure to run 'scripts/project/build_all_docker_containers.sh'!"
+
 # generate a unique id
 RUN_ID="run_$(date +%Y-%m-%d_%H-%M-%S)"
 publish_dir="resources/results/${RUN_ID}"
@@ -40,5 +43,5 @@ nextflow run openproblems-bio/task_template \
   -profile docker \
   -resume \
   -entry auto \
-  -c common/nextflow_helpers/labels.config \
+  -c common/nextflow_helpers/labels_ci.config \
   -params-file /tmp/params.yaml
diff --git a/scripts/run_benchmark/run_test_local.sh b/scripts/run_benchmark/run_test_local.sh
@@ -16,18 +16,25 @@ exit 1
 
 set -e
 
+echo "Running benchmark on test data"
+echo "  Make sure to run 'scripts/project/build_all_docker_containers.sh'!"
+
+# generate a unique id
+RUN_ID="testrun_$(date +%Y-%m-%d_%H-%M-%S)"
+publish_dir="resources/results/${RUN_ID}"
+
 # write the parameters to file
-cat > /tmp/params.yaml << 'HERE'
+cat > /tmp/params.yaml << HERE
 input_states: s3://openproblems-data/resources_test/task_template/**/state.yaml
 rename_keys: 'input_train:output_train;input_test:output_test;input_solution:output_solution'
 output_state: "state.yaml"
-publish_dir: s3://openproblems-nextflow/temp/task_template/
+publish_dir: "$publish_dir"
 HERE
 
 nextflow run . \
   -main-script target/nextflow/workflows/run_benchmark/main.nf \
   -profile docker \
   -resume \
   -entry auto \
-  -c common/nextflow_helpers/labels.config \
+  -c common/nextflow_helpers/labels_ci.config \
   -params-file /tmp/params.yaml