From 6aedad69e479596771f6c0c26dd594a95bd09ac3 Mon Sep 17 00:00:00 2001
From: Olamide Isreal <olamide@omicmd.com>
Date: Mon, 23 Mar 2026 14:51:34 +0100
Subject: [PATCH] Add nf-amazon plugin for direct S3/MinIO access

WES does not stage S3 input files to the Nextflow workdir.
Adding nf-amazon plugin so Channel.of(file(params.pdb)) can
resolve s3:// paths directly from MinIO without WES staging.
---
 nextflow.config | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/nextflow.config b/nextflow.config
index d3ab26c..5306e63 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -8,6 +8,18 @@ manifest {
     version = '1.0.0'
 }
 
+// S3/MinIO plugin for direct S3 access
+plugins {
+    id 'nf-amazon'
+}
+
+aws {
+    client {
+        endpoint = 'http://datalake-hl.datalake.svc.cluster.local:9000'
+        s3PathStyleAccess = true
+    }
+}
+
 // Global default parameters
 params {
     pdb = null