From be4db5a240b0536579e0490d4cf4553d5e9b5b61 Mon Sep 17 00:00:00 2001
From: glrs <5999366+glrs@users.noreply.github.com>
Date: Fri, 11 Oct 2024 14:56:38 +0200
Subject: [PATCH 1/3] Change the Slurm CWD to generate files in the proper
 location

---
 lib/realms/tenx/run_sample.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/realms/tenx/run_sample.py b/lib/realms/tenx/run_sample.py
index 97714ca..3c28001 100644
--- a/lib/realms/tenx/run_sample.py
+++ b/lib/realms/tenx/run_sample.py
@@ -199,7 +199,7 @@ async def process(self):
         slurm_metadata = {
             "sample_id": self.run_sample_id,
             "project_name": self.project_info.get("project_name", ""),
-            "output_dir": str(self.file_handler.sample_dir),
+            "output_dir": str(self.file_handler.base_dir),
             "cellranger_command": cellranger_command,
         }
 
@@ -258,6 +258,9 @@ def assemble_cellranger_command(self) -> str:
         required_args = self.pipeline_info.get("required_arguments", [])
         additional_args = self.pipeline_info.get("fixed_arguments", [])
 
+        # Add output directory
+        # additional_args.append(f'{"--output-dir"}={str(self.file_handler.sample_dir)}')
+
         # Mapping of argument names to their values
         arg_values: Dict[str, Any] = {
             "--id": self.run_sample_id,

From b5852108e28cca1eb58066c1b5f9c33a09071a89 Mon Sep 17 00:00:00 2001
From: glrs <5999366+glrs@users.noreply.github.com>
Date: Fri, 11 Oct 2024 16:31:08 +0200
Subject: [PATCH 2/3] Add a #NOTE for which naming to choose for original
 samples without features (default: lims id)

---
 lib/realms/tenx/tenx_project.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/lib/realms/tenx/tenx_project.py b/lib/realms/tenx/tenx_project.py
index 8b76784..f191456 100644
--- a/lib/realms/tenx/tenx_project.py
+++ b/lib/realms/tenx/tenx_project.py
@@ -289,6 +289,7 @@ def identify_feature_and_original_id_old(
             # Handle original samples without features
             library_prep_option = self.project_info.get("library_prep_option", "")
             feature = self.get_default_feature(library_prep_option)
+            # NOTE: If you want to name samples with the customer name, comment out the line below
             original_sample_id = sample_id
             return feature, original_sample_id
 
@@ -390,6 +391,7 @@ def extract_samples(self) -> List[TenXRunSample]:
         sample_data = self.filter_aborted_samples(sample_data)
         # Step 2: Create lab samples
         lab_samples = self.create_lab_samples(sample_data)
+        logging.info(f"Lab samples: {lab_samples}")
         # Step 3: Group lab samples by original sample ID
         grouped_lab_samples = self.group_lab_samples(lab_samples)
         # Step 4: Create run samples

From ba30e80e115a3a301f7426c1b63456e29ea23b51 Mon Sep 17 00:00:00 2001
From: glrs <5999366+glrs@users.noreply.github.com>
Date: Fri, 11 Oct 2024 17:24:00 +0200
Subject: [PATCH 3/3] Add output directory as a fixed argument for cellranger

---
 lib/realms/tenx/run_sample.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/realms/tenx/run_sample.py b/lib/realms/tenx/run_sample.py
index 3c28001..2ebdee5 100644
--- a/lib/realms/tenx/run_sample.py
+++ b/lib/realms/tenx/run_sample.py
@@ -258,8 +258,8 @@ def assemble_cellranger_command(self) -> str:
         required_args = self.pipeline_info.get("required_arguments", [])
         additional_args = self.pipeline_info.get("fixed_arguments", [])
 
-        # Add output directory
-        # additional_args.append(f'{"--output-dir"}={str(self.file_handler.sample_dir)}')
+        # Add output directory argument
+        additional_args.append(f"--output-dir={str(self.file_handler.sample_dir)}")
 
         # Mapping of argument names to their values
         arg_values: Dict[str, Any] = {