From 59ad63c5f6a1fd68a45ad4ce235284338c95a83c Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Mon, 26 Aug 2024 12:24:24 -0400
Subject: [PATCH] refactor: allow future user override of sing cachedir
 location

---
 src/ccbr_tools/pipeline/hpc.py      | 2 +-
 src/ccbr_tools/pipeline/nextflow.py | 7 ++++++-
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/src/ccbr_tools/pipeline/hpc.py b/src/ccbr_tools/pipeline/hpc.py
index b05ad81..54308d8 100644
--- a/src/ccbr_tools/pipeline/hpc.py
+++ b/src/ccbr_tools/pipeline/hpc.py
@@ -40,7 +40,7 @@ def __init__(self):
         self.env_vars = "\n".join(
             (
                 self.env_vars,
-                f"export PATH=${{PATH}}:/mnt/projects/CCBR-Pipelines/bin",
+                "export PATH=${PATH}:/mnt/projects/CCBR-Pipelines/bin",
             )
         )
 
diff --git a/src/ccbr_tools/pipeline/nextflow.py b/src/ccbr_tools/pipeline/nextflow.py
index ffc00f7..733be97 100644
--- a/src/ccbr_tools/pipeline/nextflow.py
+++ b/src/ccbr_tools/pipeline/nextflow.py
@@ -76,7 +76,12 @@ def run(
             "submit_slurm.sh",
             PIPELINE=pipeline_name if pipeline_name else "CCBR_nxf",
             MODULES=hpc.modules,
-            ENV_VARS=hpc.env_vars,
+            ENV_VARS="\n".join(
+                (
+                    hpc.env_vars,
+                    f"export SINGULARITY_CACHEDIR={get_singularity_cachedir()}",
+                )
+            ),  # TODO allow user override of singularity cache dir with CLI
             RUN_COMMAND=nextflow_command,
         )
         run_command = f"sbatch {slurm_filename}"