From c949564582380e7a2b9d1a5b6cee115afc008f57 Mon Sep 17 00:00:00 2001
From: jessicaw9910 <jessbwhite@gmail.com>
Date: Wed, 24 Jul 2024 22:09:48 -0400
Subject: [PATCH] update retry strategy to allow 2 retries then ignore; update
 params.max_memory to allow for up to 220GB (>3x72.GB) with 3rd process_high
 retry

---
 nextflow/main.nf         | 3 ++-
 nextflow/nextflow.config | 6 ++++--
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/nextflow/main.nf b/nextflow/main.nf
index d205d42..14c5d6e 100644
--- a/nextflow/main.nf
+++ b/nextflow/main.nf
@@ -9,7 +9,8 @@
 ----------------------------------------------------------------------------------------
 */
 
-params.max_memory = "100.GB"
+// allow 2 retries; process_high: 72.GB * task.attempt = 216.GB
+params.max_memory = "220.GB"
 params.max_cpus = 12
 
 // sub-directories - only FastQC needs additional sub-dir
diff --git a/nextflow/nextflow.config b/nextflow/nextflow.config
index 91aee25..5928fae 100644
--- a/nextflow/nextflow.config
+++ b/nextflow/nextflow.config
@@ -26,8 +26,10 @@ process {
     memory = { check_max( 6.GB * task.attempt, 'memory' ) }
     time   = { check_max( 4.h  * task.attempt, 'time'   ) }
 
-    errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
-    maxRetries    = 1
+    // https://github.com/nextflow-io/nextflow/issues/563
+    errorStrategy = {  ( task.attempt <= process.maxRetries ) ? 'retry' : 'ignore' }
+    // errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
+    maxRetries    = 2
     maxErrors     = '-1'
 
     withLabel:process_single {