Add report render script

scripts/run_benchmark/render_report_local.sh

@@ -0,0 +1,47 @@
+#!/bin/bash
+
+# fail on error
+set -e
+
+# ensure we're in the root of the repo
+REPO_ROOT=$(git rev-parse --show-toplevel)
+cd "$REPO_ROOT"
+
+# set input and output directories
+TASK=task_batch_integration
+BASE_DIR="s3://openproblems-data/resources/$TASK/results"
+OUTPUT_DIR="output/report"
+
+# find subdir in bucket with latest date
+DATE=$(aws s3 ls $BASE_DIR --recursive | awk '{print $4}' | grep 'task_info.yaml' | sort -r | head -n 1 | sed 's#.*/run_\(.*\)/[^/]*$#\1#')
+
+INPUT_DIR="$BASE_DIR/run_$DATE"
+TASK_STRIP_PREFIX=$(echo $TASK | sed 's/task_//')
+
+echo "Processing $DATE -> $OUTPUT_DIR"
+
+# start the run
+# TODO: switch to `-r build/main` once PR openproblems-bio/openproblems#919 is merged
+nextflow run openproblems-bio/openproblems \
+  -r build/feature/no-ref/update-process-results \
+  -main-script target/nextflow/reporting/process_task_results/main.nf \
+  -profile docker \
+  -resume \
+  -latest \
+  -c common/nextflow_helpers/labels_ci.config \
+  --id "$TASK/run_$DATE" \
+  --input_scores "$INPUT_DIR/score_uns.yaml" \
+  --input_dataset_info "$INPUT_DIR/dataset_uns.yaml" \
+  --input_method_configs "$INPUT_DIR/method_configs.yaml" \
+  --input_metric_configs "$INPUT_DIR/metric_configs.yaml" \
+  --input_trace "$INPUT_DIR/trace.txt" \
+  --input_task_info "$INPUT_DIR/task_info.yaml" \
+  --output_state '$id/state.yaml' \
+  --output_combined '$id/combined_output.json' \
+  --output_report '$id/report.html' \
+  --output_dataset_info '$id/dataset_info.json' \
+  --output_method_info '$id/method_info.json' \
+  --output_metric_info '$id/metric_info.json' \
+  --output_results '$id/results.json' \
+  --output_quality_control '$id/quality_control.json' \
+  --publish_dir "$OUTPUT_DIR"