From da659bc29cf02474b9e05b5adc0db8d4c2ab2740 Mon Sep 17 00:00:00 2001
From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com>
Date: Thu, 29 Feb 2024 15:27:21 -0600
Subject: [PATCH 1/7] bump to 128 gb

---
 config/process_base.config    | 5 ++++-
 modules/classify-celltypes.nf | 2 +-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/config/process_base.config b/config/process_base.config
index bd0e3c14..fe8ddf6a 100644
--- a/config/process_base.config
+++ b/config/process_base.config
@@ -1,6 +1,6 @@
 // Resource maximum settings
 params.max_cpus = 24
-params.max_memory = 96.GB
+params.max_memory = 128.GB
 
 process{
   memory = {check_memory(4.GB * task.attempt, params.max_memory)}
@@ -24,6 +24,9 @@ process{
   withLabel: mem_96 {
     memory = {check_memory(48.GB  + 48.GB * task.attempt, params.max_memory)}
   }
+  withLabel: mem_128 {
+    memory = {check_memory(64.GB + 64.GB * task.attempt, params.max_memory)}
+  }
   withLabel: cpus_2  {
     cpus = {check_cpus(2, params.max_cpus)}
   }
diff --git a/modules/classify-celltypes.nf b/modules/classify-celltypes.nf
index 5cb155d8..b7179b51 100644
--- a/modules/classify-celltypes.nf
+++ b/modules/classify-celltypes.nf
@@ -49,7 +49,7 @@ process classify_cellassign {
       mode: 'copy',
       pattern: "${cellassign_dir}"
     )
-  label 'mem_96'
+  label 'mem_128'
   label 'cpus_12'
   tag "${meta.library_id}"
   input:

From 557e623a2e30fd490bcf6a42b0725349b696a69e Mon Sep 17 00:00:00 2001
From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com>
Date: Fri, 1 Mar 2024 09:22:40 -0600
Subject: [PATCH 2/7] try 256

---
 config/process_base.config    | 4 ++--
 modules/classify-celltypes.nf | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/config/process_base.config b/config/process_base.config
index fe8ddf6a..a81543ba 100644
--- a/config/process_base.config
+++ b/config/process_base.config
@@ -24,8 +24,8 @@ process{
   withLabel: mem_96 {
     memory = {check_memory(48.GB  + 48.GB * task.attempt, params.max_memory)}
   }
-  withLabel: mem_128 {
-    memory = {check_memory(64.GB + 64.GB * task.attempt, params.max_memory)}
+  withLabel: mem_256 {
+    memory = {check_memory(128.GB + 128.GB * task.attempt, params.max_memory)}
   }
   withLabel: cpus_2  {
     cpus = {check_cpus(2, params.max_cpus)}
diff --git a/modules/classify-celltypes.nf b/modules/classify-celltypes.nf
index b7179b51..f5f7ad8c 100644
--- a/modules/classify-celltypes.nf
+++ b/modules/classify-celltypes.nf
@@ -49,7 +49,7 @@ process classify_cellassign {
       mode: 'copy',
       pattern: "${cellassign_dir}"
     )
-  label 'mem_128'
+  label 'mem_256'
   label 'cpus_12'
   tag "${meta.library_id}"
   input:

From 16b95787f0354e3e9d7a8fc3574f5bf831b06b59 Mon Sep 17 00:00:00 2001
From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com>
Date: Fri, 1 Mar 2024 16:34:16 -0600
Subject: [PATCH 3/7] 488

---
 config/process_base.config    | 6 +++---
 modules/classify-celltypes.nf | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/config/process_base.config b/config/process_base.config
index a81543ba..aa4e049d 100644
--- a/config/process_base.config
+++ b/config/process_base.config
@@ -1,6 +1,6 @@
 // Resource maximum settings
 params.max_cpus = 24
-params.max_memory = 128.GB
+params.max_memory = 488.GB
 
 process{
   memory = {check_memory(4.GB * task.attempt, params.max_memory)}
@@ -24,8 +24,8 @@ process{
   withLabel: mem_96 {
     memory = {check_memory(48.GB  + 48.GB * task.attempt, params.max_memory)}
   }
-  withLabel: mem_256 {
-    memory = {check_memory(128.GB + 128.GB * task.attempt, params.max_memory)}
+  withLabel: mem_488 {
+    memory = {check_memory(256.GB + 256.GB * task.attempt, params.max_memory)}
   }
   withLabel: cpus_2  {
     cpus = {check_cpus(2, params.max_cpus)}
diff --git a/modules/classify-celltypes.nf b/modules/classify-celltypes.nf
index f5f7ad8c..7b2e8c38 100644
--- a/modules/classify-celltypes.nf
+++ b/modules/classify-celltypes.nf
@@ -49,7 +49,7 @@ process classify_cellassign {
       mode: 'copy',
       pattern: "${cellassign_dir}"
     )
-  label 'mem_256'
+  label 'mem_488'
   label 'cpus_12'
   tag "${meta.library_id}"
   input:

From 78f719ba359537d987f39504f50bea6c5af046b7 Mon Sep 17 00:00:00 2001
From: Joshua Shapiro <josh.shapiro@ccdatalab.org>
Date: Mon, 4 Mar 2024 13:16:32 -0500
Subject: [PATCH 4/7] Bump memory for CCDL only

---
 config/process_base.config    | 4 ++--
 config/profile_ccdl.config    | 2 +-
 modules/classify-celltypes.nf | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/config/process_base.config b/config/process_base.config
index aa4e049d..969d9eb9 100644
--- a/config/process_base.config
+++ b/config/process_base.config
@@ -1,6 +1,6 @@
 // Resource maximum settings
 params.max_cpus = 24
-params.max_memory = 488.GB
+params.max_memory = 128.GB
 
 process{
   memory = {check_memory(4.GB * task.attempt, params.max_memory)}
@@ -24,7 +24,7 @@ process{
   withLabel: mem_96 {
     memory = {check_memory(48.GB  + 48.GB * task.attempt, params.max_memory)}
   }
-  withLabel: mem_488 {
+  withLabel: mem_512 {
     memory = {check_memory(256.GB + 256.GB * task.attempt, params.max_memory)}
   }
   withLabel: cpus_2  {
diff --git a/config/profile_ccdl.config b/config/profile_ccdl.config
index b50f9bf6..132fab28 100644
--- a/config/profile_ccdl.config
+++ b/config/profile_ccdl.config
@@ -18,5 +18,5 @@ params{
 
   // set max cpus and memory for internal use
   max_cpus = 64
-  max_memory = 256.GB
+  max_memory = 1024.GB
 }
diff --git a/modules/classify-celltypes.nf b/modules/classify-celltypes.nf
index 7b2e8c38..7af35ded 100644
--- a/modules/classify-celltypes.nf
+++ b/modules/classify-celltypes.nf
@@ -49,7 +49,7 @@ process classify_cellassign {
       mode: 'copy',
       pattern: "${cellassign_dir}"
     )
-  label 'mem_488'
+  label 'mem_512'
   label 'cpus_12'
   tag "${meta.library_id}"
   input:

From 16277d6525d119649920eeefe2b65a8c35d03c84 Mon Sep 17 00:00:00 2001
From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com>
Date: Thu, 7 Mar 2024 16:38:03 -0600
Subject: [PATCH 5/7] set up max_mem label

---
 config/process_base.config    | 6 +++---
 config/profile_ccdl.config    | 2 +-
 modules/classify-celltypes.nf | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/config/process_base.config b/config/process_base.config
index 969d9eb9..9610eb02 100644
--- a/config/process_base.config
+++ b/config/process_base.config
@@ -1,6 +1,6 @@
 // Resource maximum settings
 params.max_cpus = 24
-params.max_memory = 128.GB
+params.max_memory = 96.GB
 
 process{
   memory = {check_memory(4.GB * task.attempt, params.max_memory)}
@@ -24,8 +24,8 @@ process{
   withLabel: mem_96 {
     memory = {check_memory(48.GB  + 48.GB * task.attempt, params.max_memory)}
   }
-  withLabel: mem_512 {
-    memory = {check_memory(256.GB + 256.GB * task.attempt, params.max_memory)}
+  withLabel: max_mem {
+    memory = {task.attempt > 1 ? check_memory(96.GB, params.max_memory) : params.max_memory}
   }
   withLabel: cpus_2  {
     cpus = {check_cpus(2, params.max_cpus)}
diff --git a/config/profile_ccdl.config b/config/profile_ccdl.config
index 132fab28..b50f9bf6 100644
--- a/config/profile_ccdl.config
+++ b/config/profile_ccdl.config
@@ -18,5 +18,5 @@ params{
 
   // set max cpus and memory for internal use
   max_cpus = 64
-  max_memory = 1024.GB
+  max_memory = 256.GB
 }
diff --git a/modules/classify-celltypes.nf b/modules/classify-celltypes.nf
index 7af35ded..5eca31e7 100644
--- a/modules/classify-celltypes.nf
+++ b/modules/classify-celltypes.nf
@@ -49,7 +49,7 @@ process classify_cellassign {
       mode: 'copy',
       pattern: "${cellassign_dir}"
     )
-  label 'mem_512'
+  label 'max_mem'
   label 'cpus_12'
   tag "${meta.library_id}"
   input:

From f1c66280220f111982c57c518e94394cb0602c3c Mon Sep 17 00:00:00 2001
From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com>
Date: Thu, 7 Mar 2024 17:22:35 -0600
Subject: [PATCH 6/7] use the correct order for deciding memory

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

diff --git a/config/process_base.config b/config/process_base.config
index 9610eb02..8ff6493c 100644
--- a/config/process_base.config
+++ b/config/process_base.config
@@ -25,7 +25,7 @@ process{
     memory = {check_memory(48.GB  + 48.GB * task.attempt, params.max_memory)}
   }
   withLabel: max_mem {
-    memory = {task.attempt > 1 ? check_memory(96.GB, params.max_memory) : params.max_memory}
+    memory = {task.attempt > 1 ? params.max_memory : check_memory(96.GB, params.max_memory)}
   }
   withLabel: cpus_2  {
     cpus = {check_cpus(2, params.max_cpus)}

From 80b60a2077e04a6437a082a2577da6b53ddc3d4f Mon Sep 17 00:00:00 2001
From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com>
Date: Mon, 11 Mar 2024 08:57:14 -0500
Subject: [PATCH 7/7] Apply suggestions from code review

Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org>
---
 config/process_base.config    | 2 +-
 modules/classify-celltypes.nf | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/config/process_base.config b/config/process_base.config
index 8ff6493c..598b0999 100644
--- a/config/process_base.config
+++ b/config/process_base.config
@@ -24,7 +24,7 @@ process{
   withLabel: mem_96 {
     memory = {check_memory(48.GB  + 48.GB * task.attempt, params.max_memory)}
   }
-  withLabel: max_mem {
+  withLabel: mem_max {
     memory = {task.attempt > 1 ? params.max_memory : check_memory(96.GB, params.max_memory)}
   }
   withLabel: cpus_2  {
diff --git a/modules/classify-celltypes.nf b/modules/classify-celltypes.nf
index 5eca31e7..67846a73 100644
--- a/modules/classify-celltypes.nf
+++ b/modules/classify-celltypes.nf
@@ -49,7 +49,7 @@ process classify_cellassign {
       mode: 'copy',
       pattern: "${cellassign_dir}"
     )
-  label 'max_mem'
+  label 'mem_max'
   label 'cpus_12'
   tag "${meta.library_id}"
   input: