From b1269dff5c3a0e38fb817a0217a52b77f9a43842 Mon Sep 17 00:00:00 2001
From: Alexander Berger <alexander.berger@jax.org>
Date: Wed, 8 Oct 2025 15:27:44 -0400
Subject: [PATCH] Pipe generate-classifiers config json to a file

---
 nextflow/modules/jabs_classifiers.nf | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/nextflow/modules/jabs_classifiers.nf b/nextflow/modules/jabs_classifiers.nf
index 9c4162b..a08ae5f 100644
--- a/nextflow/modules/jabs_classifiers.nf
+++ b/nextflow/modules/jabs_classifiers.nf
@@ -113,12 +113,13 @@ process GENERATE_BEHAVIOR_TABLES {
         }
     ])
     """
+    echo '${behaviorJson}' > config.json
     jabs-postprocess generate-tables \
         --project-folder . \
         --feature-folder . \
         --out-prefix ${in_pose.baseName} \
         --out-bin-size 5 \
-        --behavior-config '${behaviorJson}'
+        --behavior-config ./config.json
     """
 }