Fix limma to accept spaces in variable names

modules/nf-core/limma/differential/main.nf

@@ -18,7 +18,7 @@ process LIMMA_DIFFERENTIAL {
     tuple val(meta), path("*.limma.model.txt")            , emit: model
     tuple val(meta), path("*.R_sessionInfo.log")          , emit: session_info
     tuple val(meta), path("*.normalised_counts.tsv")      , emit: normalised_counts, optional: true
-    path "versions.yml"                                   , emit: versions
+    path "versions.yml"                                   , emit: versions_limma, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/nf-core/limma/differential/meta.yml

@@ -144,6 +144,14 @@ output:
           pattern: "*.normalised_counts.tsv"
           ontologies:
             - edam: http://edamontology.org/format_3475 # TSV
+  versions_limma:
+    - 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
@@ -155,3 +163,7 @@ authors:
   - "@pinin4fjords"
 maintainers:
   - "@pinin4fjords"
+versions:
+  - versions.yml:
+      type: file
+      description: YAML file containing versions of tools used in the module

modules/nf-core/limma/differential/templates/limma_de.R

@@ -63,6 +63,80 @@ nullify <- function(x) {
   if (is.character(x) && (tolower(x) == "null" || x == "")) NULL else x
 }
 
+#' Check for Non-Empty, Non-Whitespace String
+#'
+#' This function checks if the input is non-NULL and contains more than just whitespace.
+#' It returns TRUE if the input is a non-empty, non-whitespace string, and FALSE otherwise.
+#'
+#' @param input A variable to check.
+#' @return A logical value: TRUE if the input is a valid, non-empty, non-whitespace string; FALSE otherwise.
+#' @examples
+#' is_valid_string("Hello World") # Returns TRUE
+#' is_valid_string("   ")         # Returns FALSE
+#' is_valid_string(NULL)          # Returns FALSE
+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 PARAMETERS FROM NEXTFLOW             ##
@@ -135,7 +209,11 @@ if ( ! is.null(opt\$seed)){
 }
 
 # If there is no option supplied, convert string "null" to NULL
-keys <- c("formula", "contrast_string", "contrast_variable", "reference_level", "target_level")
+keys <- c(
+    "formula", "contrast_string", "contrast_variable", "reference_level",
+    "target_level", "blocking_variables", "exclude_samples_col",
+    "exclude_samples_values", "block"
+)
 opt[keys] <- lapply(opt[keys], nullify)
 
 # Check if required parameters have been provided
@@ -225,10 +303,13 @@ if (length(missing_samples) > 0) {
 ################################################
 ################################################
 
-contrast_variable <- make.names(opt\$contrast_variable)
+contrast_variable <- NULL
 blocking.vars <- c()
+original_design_names <- NULL
 
 if (!is.null(opt\$contrast_variable)) {
+    contrast_variable <- resolve_metadata_column(opt\$contrast_variable, sample.sheet)
+
     if (!contrast_variable %in% colnames(sample.sheet)) {
         stop(
             paste0(
@@ -245,8 +326,13 @@ if (!is.null(opt\$contrast_variable)) {
             'column of the sample sheet'
             )
         )
-    } else if (!is.null(opt\$blocking_variables)) {
-        blocking.vars = make.names(unlist(strsplit(opt\$blocking_variables, split = ';')))
+    } else if (is_valid_string(opt\$blocking_variables)) {
+        blocking.vars = vapply(
+          unlist(strsplit(opt\$blocking_variables, split = ';')),
+          resolve_metadata_column,
+          character(1),
+          metadata = sample.sheet
+        )
         if (!all(blocking.vars %in% colnames(sample.sheet))) {
             missing_block <- paste(blocking.vars[! blocking.vars %in% colnames(sample.sheet)], collapse = ',')
             stop(
@@ -259,7 +345,7 @@ if (!is.null(opt\$contrast_variable)) {
     }
 
     # Handle conflicts between blocking variables and block
-    if (!is.null(opt\$block) && !is.null(opt\$blocking_variables)) {
+    if (is_valid_string(opt\$block) && is_valid_string(opt\$blocking_variables)) {
         if (opt\$block %in% blocking.vars) {
             warning(paste("Variable", opt\$block, "is specified both as a fixed effect and a random effect. It will be treated as a random effect only."))
             blocking.vars <- setdiff(blocking.vars, opt\$block)
@@ -304,11 +390,12 @@ if ((! is.null(opt\$exclude_samples_col)) && (! is.null(opt\$exclude_samples_val
 ################################################
 ################################################
 
-if (!is.null(opt\$formula)) {
+if (is_valid_string(opt\$formula)) {
     model <- opt\$formula
     model_formula <- as.formula(model)
     cat("Using user-specified formula:\n   ", deparse(model_formula), "\n")
     design <- model.matrix(model_formula, data = sample.sheet)
+    original_design_names <- colnames(design)
     colnames(design) <- make.names(colnames(design))
     cat("Column names after make.names():\n   ", paste(colnames(design), collapse = ", "), "\n")
 
@@ -338,6 +425,7 @@ if (!is.null(opt\$formula)) {
         as.formula(model),
         data=sample.sheet
     )
+    original_design_names <- colnames(design)
 
     # Adjust column names for the contrast variable
     colnames(design) <- sub(
@@ -420,9 +508,10 @@ fit <- do.call(lmFit, lmfit_args)
 # Contrasts bit
 
 # Create the contrast string for the specified comparison
-if (!is.null(opt\$contrast_string)) {
+if (is_valid_string(opt\$contrast_string)) {
     cat("Using contrast string:", opt\$contrast_string, "\n")
-    contrast_string <- as.character(opt\$contrast_string)
+    contrast_string <- normalise_contrast_string(as.character(opt\$contrast_string), original_design_names)
+    cat("Normalised contrast string:", contrast_string, "\n")
     contrast.matrix <- makeContrasts(contrasts=contrast_string, levels=colnames(design))
 
 } else {

modules/nf-core/limma/differential/tests/main.nf.test

@@ -39,7 +39,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.model, process.out.versions).match() }
+                { assert snapshot(process.out.model, process.out.versions_limma).match() }
             )
         }
     }
@@ -97,7 +97,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.model, process.out.versions).match() },
+                { assert snapshot(process.out.model, process.out.versions_limma).match() },
                 { assert path(process.out.session_info[0][1]).getText().contains("limma_3.58.1") },
                 { assert path(process.out.results[0][1]).getText().contains("1007_s_at\t-0.2775254") },
                 { assert path(process.out.results[0][1]).getText().contains("1053_at\t-0.071547786") }
@@ -159,7 +159,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.model, process.out.versions).match() },
+                { assert snapshot(process.out.model, process.out.versions_limma).match() },
                 { assert path(process.out.session_info[0][1]).getText().contains("limma_3.58.1") },
                 { assert path(process.out.results[0][1]).getText().contains("1007_s_at\t-0.27752") },
                 { assert path(process.out.results[0][1]).getText().contains("1053_at\t-0.0715477") }
@@ -221,7 +221,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.model, process.out.versions).match() },
+                { assert snapshot(process.out.model, process.out.versions_limma).match() },
                 { assert path(process.out.session_info[0][1]).getText().contains("limma_3.58.1") },
                 { assert path(process.out.results[0][1]).getText().contains("1007_s_at\t-0.4778282") },
                 { assert path(process.out.results[0][1]).getText().contains("1053_at\t-0.08958278") }
@@ -284,7 +284,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.model, process.out.versions).match() },
+                { assert snapshot(process.out.model, process.out.versions_limma).match() },
                 { assert path(process.out.session_info[0][1]).getText().contains("limma_3.58.1") },
                 { assert path(process.out.results[0][1]).getText().contains("1007_s_at\t-0.2775254") },
                 { assert path(process.out.results[0][1]).getText().contains("1053_at\t-0.071547786") }
@@ -312,7 +312,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.model, process.out.versions).match() },
+                { assert snapshot(process.out.model, process.out.versions_limma).match() },
                 { assert path(process.out.results[0][1]).getText().contains("ENSMUSG00000023978\t-4.89014922224241") },
                 { assert path(process.out.results[0][1]).getText().contains("ENSMUSG00000059991\t0.77922") },
                 { assert path(process.out.normalised_counts[0][1]).getText().contains("ENSMUSG00000023978\t6.11247620232167") },
@@ -341,7 +341,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.model, process.out.versions).match() },
+                { assert snapshot(process.out.model, process.out.versions_limma).match() },
                 { assert path(process.out.results[0][1]).getText().contains("ENSMUSG00000023978\t-2.84055986312942") },
                 { assert path(process.out.results[0][1]).getText().contains("ENSMUSG00000059991\t0.7055") },
                 { assert path(process.out.normalised_counts[0][1]).getText().contains("ENSMUSG00000023978\t6.11247620232167") },
@@ -370,7 +370,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.model, process.out.versions).match() },
+                { assert snapshot(process.out.model, process.out.versions_limma).match() },
                 { assert path(process.out.results[0][1]).getText().contains("ENSMUSG00000023978\t-2.8363444336503") },
                 { assert path(process.out.results[0][1]).getText().contains("ENSMUSG00000059991\t0.7360") },
                 { assert path(process.out.normalised_counts[0][1]).getText().contains("ENSMUSG00000023978\t6.11247620232167") },
@@ -399,7 +399,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.results, process.out.model, process.out.normalised_counts, process.out.versions).match() }
+                { assert snapshot(process.out.results, process.out.model, process.out.normalised_counts, process.out.versions_limma).match() }
             )
         }
 
@@ -423,7 +423,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot([process.out.results, process.out.model, process.out.normalised_counts, process.out.versions]).match() }            )
+                { assert snapshot([process.out.results, process.out.model, process.out.normalised_counts, process.out.versions_limma]).match() }            )
         }
     }
 }

subworkflows/nf-core/abundance_differential_filter/main.nf

@@ -94,15 +94,11 @@ workflow ABUNDANCE_DIFFERENTIAL_FILTER {
         norm_inputs.samples_and_matrix.filter{index -> index[0].differential_method == 'limma'}
     )
 
-    ch_versions = ch_versions.mix(LIMMA_NORM.out.versions.first())
-
     LIMMA_DIFFERENTIAL(
         inputs.contrasts_for_diff_with_formula.filter{index -> index[0].differential_method == 'limma' },
         inputs.samples_and_matrix.filter{index -> index[0].differential_method == 'limma' }
     )
 
-    ch_versions = ch_versions.mix(LIMMA_DIFFERENTIAL.out.versions.first())
-
     // ----------------------------------------------------
     // Run DESeq2
     // ----------------------------------------------------

subworkflows/nf-core/abundance_differential_filter/tests/main.nf.test.snap

@@ -52,15 +52,14 @@
                 "diagnosis_normal_uremia_test_limma.R_sessionInfo.log"
             ],
             [
-                "versions.yml:md5,1c02d4e455e8f3809c8ce37bee947690",
-                "versions.yml:md5,1ddaab440e2528c688c05a02dd066f12"
+                "versions.yml:md5,1c02d4e455e8f3809c8ce37bee947690"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.3"
         },
-        "timestamp": "2026-03-24T15:43:26.461974792"
+        "timestamp": "2026-03-27T16:48:42.788489896"
     },
     "deseq2 and limma - mouse - basic": {
         "content": [
@@ -264,16 +263,14 @@
             [
                 "versions.yml:md5,1a6a400c49aa4dda7ec5c4ed0cc56340",
                 "versions.yml:md5,1c02d4e455e8f3809c8ce37bee947690",
-                "versions.yml:md5,1ddaab440e2528c688c05a02dd066f12",
-                "versions.yml:md5,2c0576aefff8da32c7c0cfd8529aa4b5",
-                "versions.yml:md5,b80e2c320ea0429466a7b7c3c3ac78fa"
+                "versions.yml:md5,2c0576aefff8da32c7c0cfd8529aa4b5"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.3"
         },
-        "timestamp": "2026-03-24T15:47:16.379223242"
+        "timestamp": "2026-03-27T16:50:55.990696876"
     },
     "limma - voom": {
         "content": [
@@ -352,16 +349,14 @@
                 "treatment_mCherry_hND6_sample_number_test_limma_voom.R_sessionInfo.log"
             ],
             [
-                "versions.yml:md5,1c02d4e455e8f3809c8ce37bee947690",
-                "versions.yml:md5,1ddaab440e2528c688c05a02dd066f12",
-                "versions.yml:md5,b80e2c320ea0429466a7b7c3c3ac78fa"
+                "versions.yml:md5,1c02d4e455e8f3809c8ce37bee947690"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.3"
         },
-        "timestamp": "2026-03-24T15:45:01.909392414"
+        "timestamp": "2026-03-27T16:49:04.43670094"
     },
     "dream": {
         "content": [
@@ -674,17 +669,15 @@
             [
                 "versions.yml:md5,1a6a400c49aa4dda7ec5c4ed0cc56340",
                 "versions.yml:md5,1c02d4e455e8f3809c8ce37bee947690",
-                "versions.yml:md5,1ddaab440e2528c688c05a02dd066f12",
                 "versions.yml:md5,2c0576aefff8da32c7c0cfd8529aa4b5",
-                "versions.yml:md5,b80e2c320ea0429466a7b7c3c3ac78fa",
                 "versions.yml:md5,ff5b7c1d83470f6f548f3643bb37a830"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.3"
         },
-        "timestamp": "2026-03-24T15:48:06.008809772"
+        "timestamp": "2026-03-27T16:51:32.308588161"
     },
     "stub": {
         "content": [