From 7fbabfee3935bc0ea995438a65e610936459afb9 Mon Sep 17 00:00:00 2001
From: Olamide Isreal <olamide@omicmd.com>
Date: Mon, 16 Mar 2026 13:09:19 +0100
Subject: [PATCH] Update input/output paths to match DRS workspace
 (s3://omic/eureka/chai1)

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 main.nf     | 4 ++--
 params.json | 8 ++++----
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/main.nf b/main.nf
index 7b8d6c1..e442b72 100755
--- a/main.nf
+++ b/main.nf
@@ -1,8 +1,8 @@
 #!/usr/bin/env nextflow
 nextflow.enable.dsl=2
 
-params.input_dir = 's3://omic/eureka/chai-lab/input'
-params.outdir = 's3://omic/eureka/chai-lab/output'
+params.input_dir = 's3://omic/eureka/chai1'
+params.outdir = 's3://omic/eureka/chai1/output'
 params.use_msa = true
 params.msa_server = 'https://api.colabfold.com'
 params.num_samples = 5
diff --git a/params.json b/params.json
index 569194a..7335633 100755
--- a/params.json
+++ b/params.json
@@ -3,12 +3,12 @@
         "input_dir": {
             "type": "folder",
             "description": "Directory containing FASTA files and optional restraints",
-            "default": "s3://omic/eureka/chai-lab/input",
+            "default": "s3://omic/eureka/chai1",
             "required": true,
             "pipeline_io": "input",
             "var_name": "params.input_dir",
             "examples": [
-                "s3://omic/eureka/chai-lab/input"
+                "s3://omic/eureka/chai1"
             ],
             "pattern": ".*",
             "enum": [],
@@ -18,12 +18,12 @@
         "outdir": {
             "type": "folder",
             "description": "Directory for chai1 prediction results",
-            "default": "s3://omic/eureka/chai-lab/output",
+            "default": "s3://omic/eureka/chai1/output",
             "required": true,
             "pipeline_io": "output",
             "var_name": "params.outdir",
             "examples": [
-                "s3://omic/eureka/chai-lab/output"
+                "s3://omic/eureka/chai1/output"
             ],
             "pattern": ".*",
             "enum": [],