From 745564eafebd964a00065538f9e7490247084068 Mon Sep 17 00:00:00 2001
From: Mat Crocker <mat@formbio.com>
Date: Tue, 9 Dec 2025 11:29:26 -0600
Subject: [PATCH] feat: Add configurable MEMORY parameter to Makefile

- Add MEMORY variable with default value of 32GB
- Modify sc, ss, min, folder targets to use --memory parameter
- Allows developers to override memory: make sc MEMORY=8GB
- Helps with local development on memory-constrained systems

Usage:
  make sc              # Uses default 32GB
  make sc MEMORY=8GB   # Uses 8GB
  make sc MEMORY=16GB  # Uses 16GB
---
 Makefile | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index d01b5ff..0fb35ce 100644
--- a/Makefile
+++ b/Makefile
@@ -8,6 +8,9 @@ in_dir = test/samples
 out_dir = test/build
 fa_dir = test/fasta
 
+# Configurable parameters
+MEMORY ?= 32GB
+
 # Form Bio workflow deployment
 formbio_org := form-bio-solutions
 formbio_project := aav-qc-workshop
@@ -42,9 +45,10 @@ formbio: clean
 
 
 # Test Nextflow pipeline execution
+# Usage: make sc [MEMORY=8GB]  # Default: 32GB
 
 sc ss min folder: %: params-local-%.json
-	nextflow run -profile local main.nf -params-file $<
+	nextflow run -profile local main.nf -params-file $< --memory '$(MEMORY)'
 
 # Test local execution and outputs