From ab081ab1c9535c77ade1c013101d2753329a2cce Mon Sep 17 00:00:00 2001
From: Jaron Arbet <[jarbet@mednet.ucla.edu]>
Date: Thu, 14 Jul 2022 08:48:06 -0700
Subject: [PATCH 1/4] remove samtools sort memory restriction of 10g, causes
 errors

---
 config/F16.config | 4 +++-
 config/F32.config | 1 -
 config/F72.config | 1 -
 config/M64.config | 1 -
 4 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/config/F16.config b/config/F16.config
index 17524c2e..4fbda12d 100644
--- a/config/F16.config
+++ b/config/F16.config
@@ -15,7 +15,9 @@ process {
         }
     withName: run_sort_SAMtools {
         cpus = 12
-        memory = 10.GB
+        }
+    withName: run_merge_SAMtools {
+        cpus = 7
         }
     withName: run_MarkDuplicate_Picard {
         cpus = 1
diff --git a/config/F32.config b/config/F32.config
index aa39001b..a1b4c92b 100644
--- a/config/F32.config
+++ b/config/F32.config
@@ -15,7 +15,6 @@ process {
         }
     withName: run_sort_SAMtools {
         cpus = 12
-        memory = 10.GB
         }
     withName: run_MarkDuplicate_Picard {
         cpus = 1
diff --git a/config/F72.config b/config/F72.config
index 598ba18d..03d5c706 100644
--- a/config/F72.config
+++ b/config/F72.config
@@ -15,7 +15,6 @@ process {
         }
     withName: run_sort_SAMtools {
         cpus = 12
-        memory = 10.GB
         }
     withName: run_MarkDuplicate_Picard {
         cpus = 1
diff --git a/config/M64.config b/config/M64.config
index aa33b97b..9e79d468 100644
--- a/config/M64.config
+++ b/config/M64.config
@@ -15,7 +15,6 @@ process {
         }
     withName: run_sort_SAMtools {
         cpus = 12
-        memory = 10.GB
         }
     withName: run_MarkDuplicate_Picard {
         cpus = 1

From e8ccc3c529c37cdb354d8a83a42a374d4e3d761e Mon Sep 17 00:00:00 2001
From: Jaron Arbet <[jarbet@mednet.ucla.edu]>
Date: Thu, 21 Jul 2022 12:13:22 -0700
Subject: [PATCH 2/4] run_merge_SAMtools with 12 cpus, temporarily set
 run_sort_SAMtools to 15Gb

---
 config/F16.config | 3 ++-
 config/F32.config | 4 ++++
 config/F72.config | 4 ++++
 config/M64.config | 4 ++++
 4 files changed, 14 insertions(+), 1 deletion(-)

diff --git a/config/F16.config b/config/F16.config
index 4fbda12d..edb7cc5b 100644
--- a/config/F16.config
+++ b/config/F16.config
@@ -15,9 +15,10 @@ process {
         }
     withName: run_sort_SAMtools {
         cpus = 12
+        memory = 15.GB
         }
     withName: run_merge_SAMtools {
-        cpus = 7
+        cpus = 12
         }
     withName: run_MarkDuplicate_Picard {
         cpus = 1
diff --git a/config/F32.config b/config/F32.config
index a1b4c92b..d4653dd0 100644
--- a/config/F32.config
+++ b/config/F32.config
@@ -14,6 +14,10 @@ process {
         cpus = 32
         }
     withName: run_sort_SAMtools {
+        cpus = 12
+        memory = 15.GB
+        }
+    withName: run_merge_SAMtools {
         cpus = 12
         }
     withName: run_MarkDuplicate_Picard {
diff --git a/config/F72.config b/config/F72.config
index 03d5c706..d5b85089 100644
--- a/config/F72.config
+++ b/config/F72.config
@@ -14,6 +14,10 @@ process {
         cpus = 56
         }
     withName: run_sort_SAMtools {
+        cpus = 12
+        memory = 15.GB
+        }
+    withName: run_merge_SAMtools {
         cpus = 12
         }
     withName: run_MarkDuplicate_Picard {
diff --git a/config/M64.config b/config/M64.config
index 9e79d468..6bb64951 100644
--- a/config/M64.config
+++ b/config/M64.config
@@ -14,6 +14,10 @@ process {
         cpus = 56
         }
     withName: run_sort_SAMtools {
+        cpus = 12
+        memory = 15.GB
+        }
+    withName: run_merge_SAMtools {
         cpus = 12
         }
     withName: run_MarkDuplicate_Picard {

From ba59d15abb86e6e8b3e3854f879b1e7b659c1d2f Mon Sep 17 00:00:00 2001
From: Jaron Arbet <[jarbet@mednet.ucla.edu]>
Date: Thu, 21 Jul 2022 12:15:21 -0700
Subject: [PATCH 3/4] run_merge_SAMtools 8 cpus for F16

---
 config/F16.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/F16.config b/config/F16.config
index edb7cc5b..9693dfa8 100644
--- a/config/F16.config
+++ b/config/F16.config
@@ -18,7 +18,7 @@ process {
         memory = 15.GB
         }
     withName: run_merge_SAMtools {
-        cpus = 12
+        cpus = 8
         }
     withName: run_MarkDuplicate_Picard {
         cpus = 1

From 6d0c68b0769c8a3dbed8370b8a8af28bf276774d Mon Sep 17 00:00:00 2001
From: Jaron Arbet <[jarbet@mednet.ucla.edu]>
Date: Fri, 22 Jul 2022 08:44:25 -0700
Subject: [PATCH 4/4] run_merge_SAMtools memory 2Gb

---
 config/F16.config | 1 +
 config/F32.config | 1 +
 config/F72.config | 1 +
 config/M64.config | 1 +
 4 files changed, 4 insertions(+)

diff --git a/config/F16.config b/config/F16.config
index 9693dfa8..80aeb495 100644
--- a/config/F16.config
+++ b/config/F16.config
@@ -19,6 +19,7 @@ process {
         }
     withName: run_merge_SAMtools {
         cpus = 8
+        memory = 2.GB
         }
     withName: run_MarkDuplicate_Picard {
         cpus = 1
diff --git a/config/F32.config b/config/F32.config
index d4653dd0..cf232667 100644
--- a/config/F32.config
+++ b/config/F32.config
@@ -19,6 +19,7 @@ process {
         }
     withName: run_merge_SAMtools {
         cpus = 12
+        memory = 2.GB        
         }
     withName: run_MarkDuplicate_Picard {
         cpus = 1
diff --git a/config/F72.config b/config/F72.config
index d5b85089..6240add6 100644
--- a/config/F72.config
+++ b/config/F72.config
@@ -19,6 +19,7 @@ process {
         }
     withName: run_merge_SAMtools {
         cpus = 12
+        memory = 2.GB
         }
     withName: run_MarkDuplicate_Picard {
         cpus = 1
diff --git a/config/M64.config b/config/M64.config
index 6bb64951..914c6df1 100644
--- a/config/M64.config
+++ b/config/M64.config
@@ -19,6 +19,7 @@ process {
         }
     withName: run_merge_SAMtools {
         cpus = 12
+        memory = 2.GB
         }
     withName: run_MarkDuplicate_Picard {
         cpus = 1