From 63896148163a17b6120a916be50474c36943b0e0 Mon Sep 17 00:00:00 2001
From: Chris Rosenthal <crosenth@uw.edu>
Date: Fri, 4 Oct 2024 08:47:08 -0700
Subject: [PATCH] Adding Hutch Apptainer config settings

---
 nextflow.config | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/nextflow.config b/nextflow.config
index 470f4f8..6f8b954 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -120,6 +120,30 @@ profiles {
         }
     }
 
+    hutch_apptainer {
+        workDir = params.work_dir
+        resume = true  // null for no resume
+        apptainer {
+            enabled = true
+            autoMounts = true
+            cacheDir = '/fh/scratch/delete90/fredricks_d/lab/nhoffman/singularity/'
+        }
+        params {
+            output = 'output'
+        }
+        process {
+            container = params.container
+            executor = 'local'
+
+            // https://sciwiki.fredhutch.org/hdc/workflows/running/on_gizmo/#note-error-151
+            errorStrategy = 'retry'
+            maxRetries = 3
+        }
+        executor{
+            queueSize = 4
+        }
+    }
+
     hutch_batch {
         // choose from delete10, delete30, delete60 numbers refer to days
         workDir = "s3://fh-pi-fredricks-d-nextflow-scratch/delete10/"