From f2ab81b1a51f4f199833782d36f17c964b99c7ca Mon Sep 17 00:00:00 2001
From: ronio <roni.odai@gmail.com>
Date: Thu, 11 Jun 2026 11:41:04 +0200
Subject: [PATCH] Add toggle for db_load_mode

---
 bin/run_msa_tool.py          | 4 ++++
 modules/local/common/main.nf | 1 +
 nextflow.config              | 1 +
 tests/nextflow.config        | 1 +
 4 files changed, 7 insertions(+)

diff --git a/bin/run_msa_tool.py b/bin/run_msa_tool.py
index afb6425..fe244b3 100755
--- a/bin/run_msa_tool.py
+++ b/bin/run_msa_tool.py
@@ -51,6 +51,9 @@
 parser.add_argument(
     "--max_accept", default=100000, help="MMseqs2 max accepted alignments"
 )
+parser.add_argument("--db_load_mode", type=int, default=0,
+                    help="Database preload mode 0: auto, 1: fread, 2: mmap, 3: mmap+touch")
+
 
 args = parser.parse_args()
 
@@ -97,6 +100,7 @@
         gpu=args.gpu,
         gpu_server=args.gpu_server,
         max_accept=args.max_accept,
+        db_load_mode=args.db_load_mode,
     )
 
 
diff --git a/modules/local/common/main.nf b/modules/local/common/main.nf
index 256f2af..4f8529c 100644
--- a/modules/local/common/main.nf
+++ b/modules/local/common/main.nf
@@ -74,6 +74,7 @@ process mmseqs_align {
                         --mmseqs ${params.mmseqs_bin} \\
                         --out_dir ./ \\
                         --n_cpu ${n_cpu} \\
+                        --db_load_mode ${params.mmseqs_db_load_mode} \\
                         ${use_gpu} \\
                         ${use_env}
     fi
diff --git a/nextflow.config b/nextflow.config
index 9a961a3..18c6aec 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -31,6 +31,7 @@ params {
     mmseqs_db = "${projectDir}/database/"           // path to colabfold dbs. If installation was done as on README, no need to change anything
     mmseqs_bin = 'mmseqs'
     mmseqs_use_env = true                       // whether the environmental sequences DB should also be searched with MMseqs2
+    mmseqs_db_load_mode = 0                     // Database preload mode 0: auto, 1: fread, 2: mmap, 3: mmap+touch
 
     // general AF parameters
     af_n_gpu = 1
diff --git a/tests/nextflow.config b/tests/nextflow.config
index fff897d..6a58cf6 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -31,6 +31,7 @@ params {
     mmseqs_db = "${projectDir}/database/"           // path to colabfold dbs. If installation was done as on README, no need to change anything
     mmseqs_bin = 'mmseqs'
     mmseqs_use_env = true                       // whether the environmental sequences DB should also be searched with MMseqs2
+    mmseqs_db_load_mode = 0                     // Database preload mode 0: auto, 1: fread, 2: mmap, 3: mmap+touch
 
     // general AF parameters
     af_n_gpu = 1