Fastqc: FIX memory over-allocation (nf-core#6156)

* FIX memory over-allocation * Comment to explain why dividing by task.cpu
chelauk · Aug 22, 2024 · b49b899 · b49b899
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commit b49b899
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diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
@@ -26,7 +26,10 @@ process FASTQC {
     def rename_to = old_new_pairs*.join(' ').join(' ')
     def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
 
-    def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB')
+    // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory)
+    // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222
+    // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label
+    def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') / task.cpus
     // FastQC memory value allowed range (100 - 10000)
     def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb)
 

diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap
@@ -521,4 +521,4 @@
         },
         "timestamp": "2024-07-22T17:06:09.844235"
     }
-}
+}
-Original file line number
+Diff line change
@@ Expand Up / @@ -521,4 +521,4 @@ @@
             },
             "timestamp": "2024-07-22T17:06:09.844235"
         }
-    }
+    }