fix pipeline and scripts

scripts/run_benchmark/run_full_local.sh

@@ -0,0 +1,36 @@
+#!/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"
+
+# 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/
+
+set -e
+
+# generate a unique id
+RUN_ID="run_$(date +%Y-%m-%d_%H-%M-%S)"
+publish_dir="resources/results/${RUN_ID}"
+
+# write the parameters to file
+cat > /tmp/params.yaml << HERE
+input_states: resources/datasets/**/state.yaml
+rename_keys: 'input_singlecell_dataset:output_sc;input_spatial_dataset:output_sp'
+output_state: "state.yaml"
+publish_dir: "$publish_dir"
+HERE
+
+# run the benchmark
+nextflow run openproblems-bio/task_spatial_simulators \
+  --revision build/main \
+  -main-script target/nextflow/workflows/run_benchmark/main.nf \
+  -profile docker \
+  -resume \
+  -entry auto \
+  -c common/nextflow_helpers/labels.config \
+  -params-file /tmp/params.yaml

scripts/run_benchmark/run_full_seqeracloud.sh

@@ -0,0 +1,32 @@
+#!/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_$(date +%Y-%m-%d_%H-%M-%S)"
+publish_dir="s3://openproblems-data/resources/task_spatial_simulators/results/${RUN_ID}"
+
+# write the parameters to file
+cat > /tmp/params.yaml << HERE
+input_states: s3://openproblems-data/resources/task_spatial_simulators/datasets/**/state.yaml
+rename_keys: 'input_singlecell_dataset:output_sc;input_spatial_dataset:output_sp'
+output_state: "state.yaml"
+publish_dir: "$publish_dir"
+HERE
+
+tw launch https://github.com/openproblems-bio/task_spatial_simulators.git \
+  --revision build/main \
+  --pull-latest \
+  --main-script target/nextflow/workflows/run_benchmark/main.nf \
+  --workspace 53907369739130 \
+  --compute-env 6TeIFgV5OY4pJCk8I0bfOh \
+  --params-file /tmp/params.yaml \
+  --entry-name auto \
+  --config common/nextflow_helpers/labels_tw.config \
+  --labels task_spatial_simulators,full

scripts/run_benchmark/run_test_local.sh

@@ -0,0 +1,33 @@
+#!/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"
+
+# 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_spatial_simulators' 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
+
+# write the parameters to file
+cat > /tmp/params.yaml << 'HERE'
+input_states: s3://openproblems-data/resources_test/task_spatial_simulators/**/state.yaml
+rename_keys: 'input_singlecell_dataset:output_sc;input_spatial_dataset:output_sp'
+output_state: "state.yaml"
+publish_dir: s3://openproblems-nextflow/temp/task_spatial_simulators/
+HERE
+
+nextflow run . \
+  -main-script target/nextflow/workflows/run_benchmark/main.nf \
+  -profile docker \
+  -resume \
+  -entry auto \
+  -c common/nextflow_helpers/labels.config \
+  -params-file /tmp/params.yaml

scripts/run_benchmark/run_test_seqeracloud.sh

@@ -0,0 +1,36 @@
+#!/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"
+
+# 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_spatial_simulators' 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
+
+# write the parameters to file
+cat > /tmp/params.yaml << 'HERE'
+input_states: s3://openproblems-data/resources_test/task_spatial_simulators/**/state.yaml
+rename_keys: 'input_singlecell_dataset:output_sc;input_spatial_dataset:output_sp'
+output_state: "state.yaml"
+publish_dir: s3://openproblems-nextflow/temp/task_spatial_simulators/
+HERE
+
+tw launch https://github.com/openproblems-bio/task_spatial_simulators.git \
+  --revision build/main \
+  --pull-latest \
+  --main-script target/nextflow/workflows/run_benchmark/main.nf \
+  --workspace 53907369739130 \
+  --compute-env 6TeIFgV5OY4pJCk8I0bfOh \
+  --params-file /tmp/params.yaml \
+  --entry-name auto \
+  --config common/nextflow_helpers/labels_tw.config \
+  --labels task_spatial_simulators,test

src/workflows/run_benchmark/main.nf

@@ -128,7 +128,7 @@ workflow run_wf {
   output_ch = score_ch
 
     // extract the scores
-    | extract_metadata.run(
+    | extract_uns_metadata.run(
       key: "extract_scores",
       fromState: [input: "metric_output"],
       toState: { id, output, state ->

src/workflows/run_benchmark/test.sh

@@ -23,7 +23,7 @@ nextflow run . \
   -entry auto \
   -c common/nextflow_helpers/labels_ci.config \
   --input_states "$DATASETS_DIR/spatialsimbench_mobnew/state.yaml" \
-  --rename_keys 'input_sc:output_sc;input_sp:output_sp' \
+  --rename_keys 'input_singlecell_dataset:output_sc;input_spatial_dataset:output_sp' \
   --settings '{"output_scores": "scores.yaml", "output_dataset_info": "dataset_info.yaml", "output_method_configs": "method_configs.yaml", "output_metric_configs": "metric_configs.yaml", "output_task_info": "task_info.yaml"}' \
   --publish_dir "$OUTPUT_DIR" \
   --output_state "state.yaml"