From 4acc14269f09b6497c923085be31c5f464665d57 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Wed, 23 Mar 2022 13:42:02 -0500
Subject: [PATCH 1/3] Revise default process resource allocations

Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>
---
 conf/base.config       | 10 +++++-----
 conf/parameters.config |  4 ++--
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/conf/base.config b/conf/base.config
index ebde2c07..b3e85169 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -59,17 +59,17 @@ process {
         time   = { check_max( 4.h    * task.attempt, 'time'   ) }
     }
     withLabel:process_medium {
-        cpus   = { check_max( 6      * task.attempt, 'cpus'   ) }
+        cpus   = { check_max( 16      * task.attempt, 'cpus'   ) }
         memory = { check_max( 36.GB  * task.attempt, 'memory' ) }
-        time   = { check_max( 8.h    * task.attempt, 'time'   ) }
+        time   = { check_max( 24.h    * task.attempt, 'time'   ) }
     }
     withLabel:process_high {
-        cpus   = { check_max( 12     * task.attempt, 'cpus'   ) }
+        cpus   = { check_max( 32     * task.attempt, 'cpus'   ) }
         memory = { check_max( 72.GB  * task.attempt, 'memory' ) }
-        time   = { check_max( 16.h   * task.attempt, 'time'   ) }
+        time   = { check_max( 7.d    * task.attempt, 'time'   ) }
     }
     withLabel:process_long {
-        time   = { check_max( 20.h   * task.attempt, 'time'   ) }
+        time   = { check_max( 14.d   * task.attempt, 'time'   ) }
     }
     withLabel:process_high_memory {
         memory = { check_max( 200.GB * task.attempt, 'memory' ) }
diff --git a/conf/parameters.config b/conf/parameters.config
index dfbfc3d5..3b01f577 100644
--- a/conf/parameters.config
+++ b/conf/parameters.config
@@ -76,8 +76,8 @@ params {
 
     // Max resource options
     // Defaults only, expecting to be overwritten
-    max_memory                   = '750.GB'
-    max_cpus                     = 72
+    max_memory                   = '128.GB'
+    max_cpus                     = 32
     max_time                     = '240.h'
 
     // Step-skipping options

From 7afc7c80f5a48a28f5ca625072e0546a50655b3b Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Wed, 23 Mar 2022 13:45:21 -0500
Subject: [PATCH 2/3] Add dynamic memory allocation for Kraken2

Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>
---
 conf/modules.config | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/conf/modules.config b/conf/modules.config
index 2164878a..e58406f5 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -1,5 +1,22 @@
+import static java.lang.Math.sqrt
+import static java.lang.Math.round
+
 def platform = params.platform
 
+// Kraken memory allocation
+def kraken2_db = new File("${params.kraken2_db}")
+if (kraken2_db.isDirectory()) {
+    process {
+        withName: 'KRAKEN2' {
+            memory = {
+                def krakenDbSize = kraken2_db.directorySize()
+                def allocSize = round(sqrt(krakenDbSize) + krakenDbSize)
+                return "${allocSize} B"
+            }
+        }
+    }
+}
+
 process {
     // Deinterleaving parameter: take every other read
     withName: 'SEQKIT_SPLIT2' {

From b4637325994387555862fd653abccd4510d9cebc Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Wed, 23 Mar 2022 14:10:17 -0500
Subject: [PATCH 3/3] Bump version number

Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>
---
 CHANGELOG.md                 | 9 ++++++++-
 nextflow.config              | 2 +-
 visualizer/package-lock.json | 2 +-
 visualizer/package.json      | 2 +-
 4 files changed, 11 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5bf58b41..c6da8283 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,12 @@ Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
 
+## [0.6.4-alpha] - 2022=03-23
+
+### Fixed
+
+- Kraken2 memory allocates based on the database size again
+
 ## [0.6.3-alpha] - 2022-03-23
 
 ### Fixed
@@ -211,7 +217,8 @@ This is a major overhaul of YAVSAP to make it use nf-core's DSL2 modules.
 - Krona graphs of Kraken2 output
 - BLAST of assemblies and unclassified reads
 
-[unreleased]: https://github.com/ksumngs/yavsap/compare/v0.6.3-alpha...HEAD
+[unreleased]: https://github.com/ksumngs/yavsap/compare/v0.6.4-alpha...HEAD
+[0.6.4-alpha]: https://github.com/ksumngs/yavsap/compare/v0.6.3-alpha...v0.6.4-alpha
 [0.6.3-alpha]: https://github.com/ksumngs/yavsap/compare/v0.6.2-alpha...v0.6.3-alpha
 [0.6.2-alpha]: https://github.com/ksumngs/yavsap/compare/v0.6.1-alpha...v0.6.2-alpha
 [0.6.1-alpha]: https://github.com/ksumngs/yavsap/compare/v0.6.0-alpha...v0.6.1-alpha
diff --git a/nextflow.config b/nextflow.config
index ca4b9f08..b6899dec 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -14,7 +14,7 @@ manifest {
     description       = 'Intra-sample viral population analysis'
     mainScript        = 'main.nf'
     nextflowVersion    = '!>=21.10.6'
-    version           = '0.6.3-alpha'
+    version           = '0.6.4-alpha'
     recurseSubmodules = true
 }
 
diff --git a/visualizer/package-lock.json b/visualizer/package-lock.json
index 48a62cc9..bee8d78f 100644
--- a/visualizer/package-lock.json
+++ b/visualizer/package-lock.json
@@ -1,6 +1,6 @@
 {
   "name": "YAVSAP",
-  "version": "0.6.3-alpha",
+  "version": "0.6.4-alpha",
   "lockfileVersion": 1,
   "requires": true,
   "dependencies": {
diff --git a/visualizer/package.json b/visualizer/package.json
index da92a2ca..014fe0c9 100644
--- a/visualizer/package.json
+++ b/visualizer/package.json
@@ -1,6 +1,6 @@
 {
   "name": "YAVSAP",
-  "version": "0.6.3-alpha",
+  "version": "0.6.4-alpha",
   "repository": {
     "type": "git",
     "url": "git+https://github.com/ksumngs/yavsap.git"