From 4dcfc3f1f89d84c5fd9b224a5830ff52b56c18e1 Mon Sep 17 00:00:00 2001
From: Rahul Desai <rahul@latch.bio>
Date: Wed, 2 Oct 2024 14:27:15 -0700
Subject: [PATCH] conditionally upload .command logs

---
 latch/types/metadata.py        | 4 ++++
 latch_cli/nextflow/workflow.py | 6 +++++-
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/latch/types/metadata.py b/latch/types/metadata.py
index aebf72b8..32026ddb 100644
--- a/latch/types/metadata.py
+++ b/latch/types/metadata.py
@@ -848,6 +848,10 @@ class NextflowMetadata(LatchMetadata):
     """
     Directory to dump Nextflow logs
     """
+    upload_command_logs: bool = False
+    """
+    Upload .command.* logs to Latch Data after each task execution
+    """
     about_page_path: Optional[Path] = None
     """
     Path to a markdown file containing information about the pipeline - rendered in the About page.
diff --git a/latch_cli/nextflow/workflow.py b/latch_cli/nextflow/workflow.py
index c2297c9e..f844d6c5 100644
--- a/latch_cli/nextflow/workflow.py
+++ b/latch_cli/nextflow/workflow.py
@@ -146,8 +146,11 @@ def nextflow_runtime(pvc_name: str, {param_signature}) -> None:
             "NXF_OPTS": "-Xms{heap_initial}M -Xmx{heap_max}M -XX:ActiveProcessorCount={cpu}",
             "NXF_DISABLE_CHECK_LATEST": "true",
             "NXF_ENABLE_VIRTUAL_THREADS": "false",
-            "LATCH_LOG_DIR": latch_log_dir,
         }}
+
+        if {upload_command_logs}:
+            env["LATCH_LOG_DIR"] = latch_log_dir
+
         subprocess.run(
             cmd,
             env=env,
@@ -447,6 +450,7 @@ def generate_nextflow_workflow(
         storage_gib=resources.storage_gib,
         storage_expiration_hours=resources.storage_expiration_hours,
         log_dir=log_dir,
+        upload_command_logs=metadata._nextflow_metadata.upload_command_logs,
         nextflow_version=get_nextflow_major_version(pkg_root),
     )