Fix dream to accept spaces in variable names

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_variancepartition, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

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

@@ -92,6 +92,14 @@ output:
           pattern: "*.normalised_counts.tsv"
           ontologies:
             - edam: http://edamontology.org/format_3475 # TSV
+  versions_variancepartition:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
+topics:
   versions:
     - versions.yml:
         type: file
@@ -107,3 +115,10 @@ maintainers:
   - "@alanmmobbs03"
   - "@nschcolnicov"
   - "@atrigila"
+versions:
+  - versions.yml:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+      ontologies:
+        - edam: http://edamontology.org/format_3750 # YAML

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

@@ -23,6 +23,65 @@ is_valid_string <- function(input) {
   !is.null(input) && nzchar(trimws(input))
 }
 
+#' Rewrite a contrast expression using sanitised design column names
+#'
+#' `makeContrasts()` requires syntactically valid coefficient names. The DREAM
+#' design matrix is sanitised with `make.names()`, so a user may provide
+#' contrasts using the original names (for example containing spaces). This
+#' helper rewrites exact design-column matches to their sanitised equivalents.
+#'
+#' @param contrast_string User-provided contrast expression.
+#' @param design_names Original design matrix column names.
+#' original_design_names
+#' @return Contrast expression compatible with `makeContrasts()`.
+normalise_contrast_string <- function(contrast_string, design_names) {
+    if (!is_valid_string(contrast_string)) {
+        return(contrast_string)
+    }
+
+    sanitised_names <- make.names(design_names)
+    replacement_order <- order(nchar(design_names), decreasing = TRUE)
+    normalised <- contrast_string
+
+    for (idx in replacement_order) {
+        normalised <- gsub(
+            design_names[[idx]],
+            sanitised_names[[idx]],
+            normalised,
+            fixed = TRUE
+        )
+    }
+
+    normalised
+}
+
+#' Resolve user-supplied metadata column names against loaded metadata
+#'
+#' Metadata is read with `check.names = TRUE`, so columns containing spaces are
+#' sanitised by R. This helper accepts either the original column name or the
+#' sanitised version and returns the column present in `metadata`.
+#'
+#' @param column_name Column name provided by the user.
+#' @param metadata Loaded metadata data frame.
+#'
+#' @return Resolved column name present in metadata.
+resolve_metadata_column <- function(column_name, metadata) {
+    if (!is_valid_string(column_name)) {
+        return(column_name)
+    }
+
+    if (column_name %in% colnames(metadata)) {
+        return(column_name)
+    }
+
+    sanitised_name <- make.names(column_name)
+    if (sanitised_name %in% colnames(metadata)) {
+        return(sanitised_name)
+    }
+
+    column_name
+}
+
 #' Parse out options from a string without recourse to optparse
 #'
 #' @param x Long-form argument list like --opt1 val1 --opt2 val2
@@ -138,6 +197,8 @@ if (!is.null(opt\$seed)) {
 # Load metadata
 metadata <- read_delim_flexible(opt\$sample_file, header = TRUE, stringsAsFactors = TRUE)
 rownames(metadata) <- metadata[[opt\$sample_id_col]]
+contrast_variable <- NULL
+blocking.vars <- c()
 
 # Check if required parameters have been provided
 if (is_valid_string(opt\$formula)) {
@@ -164,8 +225,7 @@ if (length(missing) > 0) {
 }
 
 if (!is_valid_string(opt\$formula)) {
-  contrast_variable <- make.names(opt\$contrast_variable)
-  blocking.vars <- c()
+  contrast_variable <- resolve_metadata_column(opt\$contrast_variable, metadata)
 
   if (!contrast_variable %in% colnames(metadata)) {
     stop(
@@ -184,7 +244,12 @@ if (!is_valid_string(opt\$formula)) {
       )
     )
   } else if (is_valid_string(opt\$blocking_variables)) {
-    blocking.vars = make.names(unlist(strsplit(opt\$blocking_variables, split = ';')))
+    blocking.vars <- vapply(
+      unlist(strsplit(opt\$blocking_variables, split = ';')),
+      resolve_metadata_column,
+      character(1),
+      metadata = metadata
+    )
     if (!all(blocking.vars %in% colnames(metadata))) {
       missing_block <- paste(blocking.vars[! blocking.vars %in% colnames(metadata)], collapse = ',')
       stop(
@@ -199,8 +264,10 @@ if (!is_valid_string(opt\$formula)) {
 
 # Ensure contrast variable is factor, then relevel
 if (!is.null(opt\$contrast_reference) && opt\$contrast_reference != "") {
-    metadata[[opt\$contrast_variable]] <- factor(metadata[[opt\$contrast_variable]])
-    metadata[[opt\$contrast_variable]] <- relevel(metadata[[opt\$contrast_variable]], ref = opt\$contrast_reference)
+    if (!is.null(contrast_variable) && contrast_variable %in% colnames(metadata)) {
+        metadata[[contrast_variable]] <- factor(metadata[[contrast_variable]])
+        metadata[[contrast_variable]] <- relevel(metadata[[contrast_variable]], ref = opt\$contrast_reference)
+    }
 }
 
 # Exclude samples in metadata if specified
@@ -256,7 +323,7 @@ if (as.logical(opt\$apply_voom)) {
     vobjDream <- voomWithDreamWeights(dge, form, metadata, BPPARAM = bp)
 
     # Write normalized counts matrix to a TSV file
-     normalized_counts <- vobjDream\$E
+    normalized_counts <- vobjDream\$E
     if (!is.null(opt\$round_digits)) {
         normalized_counts <- apply(normalized_counts, 2, function(x) round(x, opt\$round_digits))
     }
@@ -302,7 +369,11 @@ if (!is.null(opt\$contrast_string)) {
 if (is_valid_string(contrast_string)) {
     cat("Using contrast string:", contrast_string, "\n")
 
-    colnames(fitmm\$design) <- make.names(colnames(fitmm\$design))
+    original_design_names <- colnames(fitmm\$design)
+    colnames(fitmm\$design) <- make.names(original_design_names)
+    contrast_string <- normalise_contrast_string(contrast_string, original_design_names)
+    cat("Normalised contrast string:", contrast_string, "\n")
+
     contrast_matrix <- makeContrasts(contrast = contrast_string, levels = colnames(fitmm\$design))
     fit2 <- contrasts.fit(fitmm, contrast_matrix)
     fit2 <- eBayes(fit2, proportion = opt\$proportion,

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

@@ -41,7 +41,7 @@ nextflow_process {
                 { assert path(process.out.results[0][1]).getText().contains("gene_id\tlogFC\tAveExpr\tt\tP.Value\tadj.P.Val\tB") },
                 { assert path(process.out.results[0][1]).getText().contains("1309.83") },
                 { assert path(process.out.results[0][1]).getText().contains("557\t279.88\t18.81") },
-                { assert snapshot(process.out.model, process.out.versions).match() }
+                { assert snapshot(process.out.model, process.out.versions_variancepartition).match() }
             )
         }
     }
@@ -77,7 +77,7 @@ nextflow_process {
                 { assert path(process.out.results[0][1]).getText().contains("gene_id\tlogFC\tAveExpr\tt\tP.Value\tadj.P.Val\tB") },
                 { assert path(process.out.results[0][1]).getText().contains("5.07") },
                 { assert path(process.out.results[0][1]).getText().contains("2.97\t3.88\t38.17") },
-                { assert snapshot(process.out.model, process.out.normalised_counts, process.out.versions).match() }
+                { assert snapshot(process.out.model, process.out.normalised_counts, process.out.versions_variancepartition).match() }
             )
         }
     }
@@ -111,7 +111,7 @@ nextflow_process {
                 { assert path(process.out.results[0][1]).getText().contains("gene_id\tlogFC\tAveExpr\tt\tP.Value\tadj.P.Val\tB") },
                 { assert path(process.out.results[0][1]).getText().contains("-849.67") },
                 { assert path(process.out.results[0][1]).getText().contains("-1050\t549\t-3.78") },
-                { assert snapshot(process.out.model, process.out.versions).match() }
+                { assert snapshot(process.out.model, process.out.versions_variancepartition).match() }
             )
         }
     }
@@ -146,7 +146,7 @@ nextflow_process {
                 { assert path(process.out.results[0][1]).getText().contains("gene_id\tlogFC\tAveExpr\tt\tP.Value\tadj.P.Val\tB") },
                 { assert path(process.out.results[0][1]).getText().contains("1050") },
                 { assert path(process.out.results[0][1]).getText().contains("849.67\t432.83\t3.8") },
-                { assert snapshot(process.out.model, process.out.versions).match() }
+                { assert snapshot(process.out.model, process.out.versions_variancepartition).match() }
             )
         }
     }
@@ -180,7 +180,7 @@ nextflow_process {
                 { assert path(process.out.results[0][1]).getText().contains("gene_id\tlogFC\tAveExpr\tt\tP.Value\tadj.P.Val\tB") },
                 { assert path(process.out.results[0][1]).getText().contains("2124\t549\t4.84") },
                 { assert path(process.out.results[0][1]).getText().contains("1707.33") },
-                { assert snapshot(process.out.model, process.out.versions).match() }
+                { assert snapshot(process.out.model, process.out.versions_variancepartition).match() }
             )
         }
     }
@@ -211,7 +211,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.model, process.out.versions).match() },
+                { assert snapshot(process.out.model, process.out.versions_variancepartition).match() },
                 { assert path(process.out.results[0][1]).getText().contains("gene_id\tlogFC\tAveExpr\tt\tP.Value\tadj.P.Val\tB") },
                 { assert path(process.out.results[0][1]).getText().contains("-95.67") },
                 { assert path(process.out.results[0][1]).getText().contains("1050\t549\t4.16") }

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": [
@@ -279,16 +279,16 @@
                         "treatment_mCherry_hND6.dream.results.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
+                "versions_variancepartition": [
                     "versions.yml:md5,03b686ec8c67a91501ebb2b2a5234e77"
                 ]
             }
         ],
-        "timestamp": "2026-01-13T15:35:07.121696674",
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.04.2"
-        }
+            "nextflow": "25.10.3"
+        },
+        "timestamp": "2026-03-27T17:37:18.306234608"
     },
     "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": [
@@ -374,16 +374,16 @@
                         "genotype_WT_KO_treatment_Control_Treated.dream.results.tsv:md5,90a06e6b4945c706025582a4c9fddf2c"
                     ]
                 ],
-                "versions": [
+                "versions_variancepartition": [
                     "versions.yml:md5,fc1f26eb2194018e99fc2916332676b7"
                 ]
             }
         ],
-        "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": "2026-03-27T17:37:36.063080982"
     },
     "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"
     }
 }

subworkflows/nf-core/abundance_differential_filter/main.nf

@@ -172,8 +172,6 @@ workflow ABUNDANCE_DIFFERENTIAL_FILTER {
         inputs.samples_and_matrix.filter{index -> index[0].differential_method == 'dream' }
     )
 
-    ch_versions = ch_versions.mix( VARIANCEPARTITION_DREAM.out.versions.first() )
-
     // ----------------------------------------------------
     // Collect results
     // ----------------------------------------------------