From 3e74a9f82ee4e1c2767650e576aff09e1018a538 Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Mon, 27 Jul 2026 08:51:10 +0200
Subject: [PATCH] Add denbi script

---
 common                                  |  2 +-
 scripts/run_benchmark/run_full_denbi.sh | 32 +++++++++++++++++++++++++
 2 files changed, 33 insertions(+), 1 deletion(-)
 create mode 100755 scripts/run_benchmark/run_full_denbi.sh

diff --git a/common b/common
index b505fd6..d961b8b 160000
--- a/common
+++ b/common
@@ -1 +1 @@
-Subproject commit b505fd616154190db807490589cb42b5e8b32192
+Subproject commit d961b8b13a14b5f6b9c75bdc4bde1c5c5faf657f
diff --git a/scripts/run_benchmark/run_full_denbi.sh b/scripts/run_benchmark/run_full_denbi.sh
new file mode 100755
index 0000000..3dcdb89
--- /dev/null
+++ b/scripts/run_benchmark/run_full_denbi.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_$(date +%Y-%m-%d_%H-%M-%S)"
+publish_dir="/vol/scratch/results/task_predict_modality/${RUN_ID}"
+
+# write the parameters to file
+cat > /tmp/params.yaml << HERE
+input_states: "s3://openproblems-data/resources/task_predict_modality/datasets/**/state.yaml"
+rename_keys: "input_train_mod1:output_train_mod1;input_train_mod2:output_train_mod2;input_test_mod1:output_test_mod1;input_test_mod2:output_test_mod2"
+output_state: "state.yaml"
+publish_dir: "$publish_dir"
+HERE
+
+tw launch https://github.com/openproblems-bio/task_predict_modality.git \
+  --revision build/main \
+  --pull-latest \
+  --main-script target/nextflow/workflows/run_benchmark/main.nf \
+  --workspace 53907369739130 \
+  --compute-env 3qstFmP9lNwdzutSNuJq7c \
+  --params-file /tmp/params.yaml \
+  --entry-name auto \
+  --config common/nextflow_helpers/labels_denbi.config \
+  --labels task_predict_modality,full,denbi