From 31dd98ee9a4deb6115741e70770316bbfd49f662 Mon Sep 17 00:00:00 2001
From: Aaron Petkau <aaron.petkau@gmail.com>
Date: Thu, 25 Jan 2024 16:02:43 -0600
Subject: [PATCH] Added ability to limit network connections

---
 conf/modules.config  |  4 ++++
 nextflow.config      | 13 ++++++++-----
 nextflow_schema.json |  6 ++++++
 3 files changed, 18 insertions(+), 5 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index c6ad44a..2d40329 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -25,4 +25,8 @@ process {
             pattern: '*_versions.yml'
         ]
     }
+
+    withName: SRATOOLS_PREFETCH {
+        maxForks = params.max_jobs_with_network_connections
+    }
 }
diff --git a/nextflow.config b/nextflow.config
index 3d6f102..61db778 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -37,11 +37,14 @@ params {
     max_time                   = '1.h'
 
     // Schema validation default options
-    validationFailUnrecognisedParams = false
-    validationLenientMode            = false
-    validationSchemaIgnoreParams     = 'genomes,igenomes_base'
-    validationShowHiddenParams       = false
-    validate_params                  = true
+    validationFailUnrecognisedParams  = false
+    validationLenientMode             = false
+    validationSchemaIgnoreParams      = 'genomes,igenomes_base'
+    validationShowHiddenParams        = false
+    validate_params                   = true
+
+    // Options for limiting network activity
+    max_jobs_with_network_connections = 1
 }
 
 // Load base.config by default for all pipelines
diff --git a/nextflow_schema.json b/nextflow_schema.json
index bb6905e..8a30502 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -190,6 +190,12 @@
                     "description": "Validation of parameters in lenient more.",
                     "hidden": true,
                     "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)."
+                },
+                "max_jobs_with_network_connections": {
+                    "type": "integer",
+                    "default": 1,
+                    "description": "Maximum number of jobs with network connections allowed to run at once",
+                    "hidden": true
                 }
             }
         }