From c6b354f1aeb259e93022d77a2cf0cf99fa7ae894 Mon Sep 17 00:00:00 2001
From: Jocelyn <penington.j@wehi.edu.au>
Date: Fri, 31 May 2024 15:11:26 +1000
Subject: [PATCH] add label for bamfile indexing and increase memory

---
 config/modules.config | 10 +++++++++-
 modules/bwa.nf        |  2 +-
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/config/modules.config b/config/modules.config
index 97dc312..b597bba 100644
--- a/config/modules.config
+++ b/config/modules.config
@@ -16,11 +16,19 @@ process {
     withLabel:BWAAlign {
         queue='regular'
         cpus = 5
-        memory={ 8.GB * task.attempt }
+        memory={ 4.GB * task.attempt }
         time='12h'
         errorStrategy ={ 'retry'  }
         maxRetries= 5
     }
+    withLabel:IndexDedup {
+        queue='regular'
+        cpus = 5
+        memory={ 8.GB * task.attempt }
+        time='8h'
+        errorStrategy ={ 'retry'  }
+        maxRetries= 5
+    }
     withLabel:Write {
         queue='regular'
         cpus = 1
diff --git a/modules/bwa.nf b/modules/bwa.nf
index c5f375b..cb1bfc8 100644
--- a/modules/bwa.nf
+++ b/modules/bwa.nf
@@ -22,7 +22,7 @@ process Bwa {
 }
 
 process Index {
-    label 'BWAAlign'
+    label 'IndexDedup'
     tag "${sampleId}"
     publishDir "${params.outdir}/align", mode: 'copy'