Merge branch 'hotfix/0.6.4-alpha'

ksumngs · Mar 23, 2022 · bededa6 · bededa6
2 parents d76eee3 + b463732
commit bededa6
Show file tree

Hide file tree

Showing 7 changed files with 35 additions and 11 deletions.
diff --git 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/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/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' {

diff --git 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

diff --git 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
diff --git 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"