Merge pull request #165 from uclahs-cds/sfitz-adjust-learnReadOrienta…

…tin-mem Increase memory for GATK LearnReadOrientation and cpu 1
uclahs-cds · Apr 5, 2023 · 7976a54 · 7976a54
2 parents 068ba1f + 3cfa1bf
commit 7976a54
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,15 +5,22 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
+
 ### Added
 - Add Mutect2 flow chart
 - Add plantUML action and MuSE flow chart
 - Add NF-test
+
 ### Changed
+- Update LearnRaadOrientationModel allocated memory
+- Update to use `MuSE` v2.0.1 with `MuSE sump` parallelization
 - Update to GATK v4.4.0.0
 - Update `MuSE` retry add memory to 48GB
 - Changed `output_dir` to `output_dir_base` (`methods.config` and `main.nf`)
 
+### Fixed
+- Specify empty string as default for bgzip and tabix extra args
+
 ## [6.0.0-rc.1] - 2023-02-08
 ### Changed
 - Update `README`: add Pipeline Steps and Tool descriptions

diff --git a/config/F16.config b/config/F16.config
@@ -60,8 +60,8 @@ process {
         }
     }
     withName: run_LearnReadOrientationModel_GATK {
-        cpus = 4
-        memory = 8.GB
+        cpus = 1
+        memory = 16.GB
         retry_strategy {
             memory {
                 strategy = 'exponential'

diff --git a/config/F32.config b/config/F32.config
@@ -60,8 +60,8 @@ process {
         }
     }
     withName: run_LearnReadOrientationModel_GATK {
-        cpus = 4
-        memory = 8.GB
+        cpus = 1
+        memory = 16.GB
         retry_strategy {
             memory {
                 strategy = 'exponential'

diff --git a/config/F72.config b/config/F72.config
@@ -59,8 +59,8 @@ process {
         }
     }
     withName: run_LearnReadOrientationModel_GATK {
-        cpus = 4
-        memory = 8.GB
+        cpus = 1
+        memory = 16.GB
         retry_strategy {
             memory {
                 strategy = 'exponential'

diff --git a/config/schema.yaml b/config/schema.yaml
@@ -66,6 +66,18 @@ filter_mutect_calls_extra_args:
   required: false
   allow_empty: true
   help: 'Additional arguments for the FilterMutectCalls command'
+bgzip_extra_args:
+  type: 'String'
+  required: false
+  allow_empty: true
+  default: ''
+  help: 'Additional arguments for bgzip command'
+tabix_extra_args:
+  type: 'String'
+  required: false
+  allow_empty: true
+  default: ''
+  help: 'Additional arguments for tabix command'
 scatter_count:
   type: 'Integer'
   required: true