Merge pull request #647 from FriederikeHanssen/resource_labels

Resource Labels
nf-core · Jul 19, 2022 · 1e043d3 · 1e043d3
2 parents d840af4 + c7c4d27
commit 1e043d3
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -43,6 +43,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#632](https://github.com/nf-core/sarek/pull/632) - Added params `--snpeff_version` to allow more configuration on the snpeff container definition
 - [#632](https://github.com/nf-core/sarek/pull/632) - Added params `--vep_include_fasta` to use the fasta file for annotation
 - [#639](https://github.com/nf-core/sarek/pull/639) - Adding genes-txt-file and summary-html-file to the published output from snpEff.
+- [#647](https://github.com/nf-core/sarek/pull/647) - Update resource requests for preprocessing based on what worked for 5 ICGC matched WGS samples
 - [#652](https://github.com/nf-core/sarek/pull/652) - Added full size somatic test profile.
 
 ### Changed

diff --git a/conf/base.config b/conf/base.config
@@ -49,8 +49,28 @@ process {
         errorStrategy = 'retry'
         maxRetries    = 2
     }
-    withName: 'BWAMEM2_MEM' {
-        memory       = { check_max( 60.GB * task.attempt, 'memory' ) }
+    withName: 'BWAMEM1_MEM|BWAMEM2_MEM' {
+        cpus         = { check_max( 24 * task.attempt, 'cpus' ) }
+        memory       = { check_max( 36.GB * task.attempt, 'memory' ) }
         time         = { check_max( 48.h  * task.attempt, 'time'    ) }
     }
+    withName: 'FASTP'{
+        cpus         = { check_max( 12 * task.attempt, 'cpus' ) }
+    }
+    withName:'FASTQC|FASTP|MOSDEPTH|SAMTOOLS_CONVERT|SAMTOOLS_MERGE'{
+        memory       = { check_max( 4.GB * task.attempt, 'memory' ) }
+    }
+    withName:'GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK|GATK4_BASERECALIBRATOR|SAMTOOLS_STATS'{
+        cpus         = { check_max( 4 * task.attempt, 'cpus' ) }
+    }
+    withName:'GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK|GATK4_BASERECALIBRATOR|GATK4_GATHERBQSRREPORTS'{
+        memory       = { check_max( 46.GB * task.attempt, 'memory' ) }
+    }
+    withName: 'GATK4_MARKDUPLICATES'{
+        memory       = { check_max( 300.GB * task.attempt, 'memory' ) }
+    }
+    withName: 'FREEBAYES|SAMTOOLS_STATS|SAMTOOLS_INDEX|UNZIP' {
+        cpus         = { check_max( 1 * task.attempt, 'cpus'    ) }
+    }
+
 }