refactor: allow future user override of sing cachedir location

CCBR · Aug 26, 2024 · 59ad63c · 59ad63c
1 parent eaf946d
commit 59ad63c
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Showing 2 changed files with 7 additions and 2 deletions.
diff --git 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
@@ -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}"