Update run full benchmark scripts

scripts/run_benchmark/run_full_local.sh

@@ -12,12 +12,12 @@ cd "$REPO_ROOT"
 # 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_template' 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
+# echo "TODO: once the 'run_benchmark' workflow has been implemented, update this script to use it."
+# echo "  Step 1: replace 'task_template' 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
 
@@ -31,13 +31,13 @@ publish_dir="resources/results/${RUN_ID}"
 # write the parameters to file
 cat > /tmp/params.yaml << HERE
 input_states: resources/datasets/**/state.yaml
-rename_keys: 'input_train:output_train;input_test:output_test;input_solution:output_solution'
+rename_keys: 'input_dataset:output_dataset;input_solution:output_solution'
 output_state: "state.yaml"
 publish_dir: "$publish_dir"
 HERE
 
 # run the benchmark
-nextflow run openproblems-bio/task_template \
+nextflow run openproblems-bio/task_dimensionality_reduction \
   --revision build/main \
   -main-script target/nextflow/workflows/run_benchmark/main.nf \
   -profile docker \

scripts/run_benchmark/run_full_seqeracloud.sh

@@ -7,28 +7,28 @@ REPO_ROOT=$(git rev-parse --show-toplevel)
 cd "$REPO_ROOT"
 
 # 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_template' 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
+# echo "TODO: once the 'run_benchmark' workflow has been implemented, update this script to use it."
+# echo "  Step 1: replace 'task_template' 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
 
 # generate a unique id
 RUN_ID="run_$(date +%Y-%m-%d_%H-%M-%S)"
-publish_dir="s3://openproblems-data/resources/task_template/results/${RUN_ID}"
+publish_dir="s3://openproblems-data/resources/task_dimensionality_reduction/results/${RUN_ID}"
 
 # write the parameters to file
 cat > /tmp/params.yaml << HERE
-input_states: s3://openproblems-data/resources/task_template/datasets/**/state.yaml
-rename_keys: 'input_train:output_train;input_test:output_test;input_solution:output_solution'
+input_states: s3://openproblems-data/resources/task_dimensionality_reduction/datasets/**/state.yaml
+rename_keys: 'input_dataset:output_dataset;input_solution:output_solution'
 output_state: "state.yaml"
 publish_dir: "$publish_dir"
 HERE
 
-tw launch https://github.com/openproblems-bio/task_template.git \
+tw launch https://github.com/openproblems-bio/task_dimensionality_reduction.git \
   --revision build/main \
   --pull-latest \
   --main-script target/nextflow/workflows/run_benchmark/main.nf \
@@ -37,4 +37,4 @@ tw launch https://github.com/openproblems-bio/task_template.git \
   --params-file /tmp/params.yaml \
   --entry-name auto \
   --config common/nextflow_helpers/labels_tw.config \
-  --labels task_template,full
+  --labels task_dimensionality_reduction,full