Disable implicit parallelism in variancepartition/dream

modules/nf-core/variancepartition/dream/main.nf

@@ -15,7 +15,7 @@ process VARIANCEPARTITION_DREAM {
     tuple val(meta), path("*.dream.results.tsv")        , emit: results
     tuple val(meta), path("*.dream.model.txt")          , emit: model
     tuple val(meta), path("*.normalised_counts.tsv")    , emit: normalised_counts, optional: true
-    path "versions.yml"                                 , emit: versions
+    path "versions.yml"                                 , emit: versions, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/nf-core/variancepartition/dream/meta.yml

@@ -99,6 +99,11 @@ output:
         pattern: "versions.yml"
         ontologies:
           - edam: http://edamontology.org/format_3750 # YAML
+topics:
+  versions:
+    - versions.yml:
+        type: string
+        description: The name of the process
 authors:
   - "@alanmmobbs03"
   - "@nschcolnicov"

modules/nf-core/variancepartition/dream/templates/dream.R

@@ -82,6 +82,7 @@ opt <- list(
     contrast_string            = "$comparison",           # Full (complex) contrast expression comparison needed if using formula
     sample_id_col              = "sample",                # Column name for sample IDs
     threads                    = "$task.cpus",            # Number of threads for multithreading
+    blas_threads               = 1,                       # Number of threads for BLAS/OpenMP backends
     subset_to_contrast_samples = FALSE,                   # Whether to subset to contrast samples
     exclude_samples_col        = NULL,                    # Column for excluding samples
     exclude_samples_values     = NULL,                    # Values for excluding samples
@@ -116,6 +117,7 @@ keys <- c("formula", "contrast_string", "contrast_target", "contrast_variable",
 opt[keys] <- lapply(opt[keys], nullify)
 
 opt\$threads      <- as.numeric(opt\$threads)
+opt\$blas_threads <- as.numeric(opt\$blas_threads)
 opt\$apply_voom   <- as.logical(opt\$apply_voom)
 opt\$proportion   <- as.numeric(opt\$proportion)
 opt\$trend        <- as.logical(opt\$trend)
@@ -135,6 +137,32 @@ if (!is.null(opt\$seed)) {
   set.seed(opt\$seed)
 }
 
+if (is.na(opt\$blas_threads) || opt\$blas_threads < 1) {
+  stop("'blas_threads' must be a positive integer")
+}
+opt\$blas_threads <- as.integer(opt\$blas_threads)
+
+configure_blas_threads <- function(threads) {
+  thread_env <- c(
+    OPENBLAS_NUM_THREADS = threads,
+    OMP_NUM_THREADS = threads,
+    MKL_NUM_THREADS = threads,
+    BLIS_NUM_THREADS = threads,
+    VECLIB_MAXIMUM_THREADS = threads,
+    NUMEXPR_NUM_THREADS = threads
+  )
+  do.call(Sys.setenv, as.list(thread_env))
+
+  if (requireNamespace("RhpcBLASctl", quietly = TRUE)) {
+    RhpcBLASctl::blas_set_num_threads(threads)
+    RhpcBLASctl::omp_set_num_threads(threads)
+  }
+
+  cat("Configured implicit BLAS/OpenMP threads to", threads, "\n")
+}
+
+configure_blas_threads(opt\$blas_threads)
+
 # Load metadata
 metadata <- read_delim_flexible(opt\$sample_file, header = TRUE, stringsAsFactors = TRUE)
 rownames(metadata) <- metadata[[opt\$sample_id_col]]

modules/nf-core/variancepartition/dream/tests/main.nf.test.snap

@@ -15,11 +15,11 @@
                 "versions.yml:md5,fc1f26eb2194018e99fc2916332676b7"
             ]
         ],
-        "timestamp": "2025-12-23T18:57:51.598745459",
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.04.2"
-        }
+        },
+        "timestamp": "2025-12-23T18:57:51.598745459"
     },
     "RNAseq - Feature Counts - formula + comparison contrast string - interaction": {
         "content": [
@@ -37,11 +37,11 @@
                 "versions.yml:md5,fc1f26eb2194018e99fc2916332676b7"
             ]
         ],
-        "timestamp": "2025-12-26T15:10:51.980662299",
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.04.2"
-        }
+        },
+        "timestamp": "2025-12-26T15:10:51.980662299"
     },
     "Mus musculus - contrasts - matrix - no formula": {
         "content": [
@@ -61,11 +61,11 @@
                 "versions.yml:md5,fc1f26eb2194018e99fc2916332676b7"
             ]
         ],
-        "timestamp": "2025-12-16T15:52:08.047223666",
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
-        }
+        },
+        "timestamp": "2025-12-16T15:52:08.047223666"
     },
     "Mus musculus - expression table - contrasts + blocking factors": {
         "content": [
@@ -130,11 +130,11 @@
                 ]
             }
         ],
-        "timestamp": "2025-12-16T19:59:57.947286403",
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
-        }
+        },
+        "timestamp": "2025-12-16T19:59:57.947286403"
     },
     "Mus musculus - expression table - contrasts + blocking factors stub": {
         "content": [
@@ -199,11 +199,11 @@
                 ]
             }
         ],
-        "timestamp": "2025-11-10T16:18:37.294899756",
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
-        }
+        },
+        "timestamp": "2025-11-10T16:18:37.294899756"
     },
     "Mus musculus - expression table - contrasts + formula + weighted comparison contrast string": {
         "content": [
@@ -221,11 +221,11 @@
                 "versions.yml:md5,fc1f26eb2194018e99fc2916332676b7"
             ]
         ],
-        "timestamp": "2025-12-23T18:57:42.761838155",
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.04.2"
-        }
+        },
+        "timestamp": "2025-12-23T18:57:42.761838155"
     },
     "Mus musculus - expression table - contrasts + formula + comparison contrast string - no intercept stub": {
         "content": [
@@ -284,11 +284,11 @@
                 ]
             }
         ],
-        "timestamp": "2026-01-13T15:35:07.121696674",
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.04.2"
-        }
+        },
+        "timestamp": "2026-01-13T15:35:07.121696674"
     },
     "RNAseq - Voom - Feature Counts - formula + comparison contrast string - interaction": {
         "content": [
@@ -316,11 +316,11 @@
                 "versions.yml:md5,fc1f26eb2194018e99fc2916332676b7"
             ]
         ],
-        "timestamp": "2026-01-13T15:53:31.743589111",
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.04.2"
-        }
+        },
+        "timestamp": "2026-01-13T15:53:31.743589111"
     },
     "RNAseq - Feature Counts - formula + comparison contrast string - interaction with seed": {
         "content": [
@@ -379,11 +379,11 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-25T21:03:52.327619963",
         "meta": {
-            "nf-test": "0.9.5",
-            "nextflow": "25.10.4"
-        }
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.3"
+        },
+        "timestamp": "2026-05-07T19:32:24.587570625"
     },
     "Mus musculus - expression table - contrasts + formula + comparison contrast string": {
         "content": [
@@ -401,10 +401,10 @@
                 "versions.yml:md5,fc1f26eb2194018e99fc2916332676b7"
             ]
         ],
-        "timestamp": "2025-12-26T15:11:01.472042429",
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.04.2"
-        }
+        },
+        "timestamp": "2025-12-26T15:11:01.472042429"
     }
 }