Increase resouces for FastQC and fastq screen (#62)

* Increase resouces for FastQC and fastq screen * Add increased resources as label instead
Molmed · Sep 3, 2024 · ed7490c · ed7490c
1 parent a6624f4
commit ed7490c
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Showing 3 changed files with 11 additions and 5 deletions.
diff --git a/config/nextflow_config/compute_resources.config b/config/nextflow_config/compute_resources.config
@@ -3,13 +3,14 @@ process {
         time = '12h'
     }
     withName: 'FASTQ_SCREEN' {
-        memory = '4G'
         time = '12h'
+        memory = '4G'
     }
     withName: 'GET_QC_THRESHOLDS' {
         errorStrategy = 'ignore'
     }
-    withLabel: 'high_memory' {
+    withLabel: 'high_memory_and_cpus' {
         memory = '47G'
+        cpus = 8
     }
 }
diff --git a/main.nf b/main.nf
@@ -167,6 +167,8 @@ workflow CHECK_RUN_QUALITY {
 
 process FASTQC {
 
+    label 'high_memory_and_cpus'
+
     input:
     tuple val(project), path(fastq_file)
     path config_dir
@@ -183,6 +185,8 @@ process FASTQC {
 
 process FASTQ_SCREEN {
 
+    label 'high_memory_and_cpus'
+
     input:
     tuple val(project), path(fastq_file)
     path config_dir
@@ -271,7 +275,7 @@ process INTEROP_SUMMARY {
 process MULTIQC_PER_FLOWCELL {
 
     publishDir "${params.result_dir}/flowcell_report", mode: 'copy', overwrite: true
-    label 'high_memory'
+    label 'high_memory_and_cpus'
 
     input:
     val runfolder_name              // Run folder name

diff --git a/nextflow.config b/nextflow.config
@@ -17,10 +17,11 @@ profiles {
         executor.memory = '12G'
         includeConfig "$baseDir/config/nextflow_config/compute_resources.config"
 
-        // Overwrite high_memory label
+        // Overwrite high_memory_and_cpus label
         process {
-            withLabel: 'high_memory' {
+            withLabel: 'high_memory_and_cpus' {
                 memory = '12G'
+                cpus = 1
             }
         }
     }