From fdbd7bf863febcfa7e33d597b2e7e16b7335dc29 Mon Sep 17 00:00:00 2001
From: Olamide Isreal <olamide@omicmd.com>
Date: Mon, 16 Mar 2026 19:54:59 +0100
Subject: [PATCH] Use dedicated input subdirectory to avoid stale files

Previous runs left rcsb_pdb_1QGS.fasta in the work dir.
Using s3://omic/eureka/chai1/input/ ensures only our files are picked up.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index b050d64..9989703 100755
--- a/main.nf
+++ b/main.nf
@@ -1,7 +1,7 @@
 #!/usr/bin/env nextflow
 nextflow.enable.dsl=2
 
-params.input_dir = 's3://omic/eureka/chai1'
+params.input_dir = 's3://omic/eureka/chai1/input'
 params.outdir = 's3://omic/eureka/chai1/output'
 params.use_msa = true
 params.msa_server = 'https://api.colabfold.com'