Merge pull request #513 from nf-core/fix-contrast-schema

Allow zero-intercept models in contrasts schema

Author: grst

CHANGELOG.md

@@ -27,6 +27,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
+- [[#513](https://github.com/nf-core/differentialabundance/pull/513)] - Fix contrast schema to allow for zero-intercept models. ([@grst](https://github.com/grst), review by [@pinin4fjords](https://github.com/pinin4fjords)).
 - [[#476](https://github.com/nf-core/differentialabundance/pull/476)] - Fixed null.csv and warning at top of report ([@SusiJo](https://github.com/SusiJo), reviewed by [@pinin4fjords](https://github.com/pinin4fjords), [@atrigila](https://github.com/atrigila), [@maxulysse](https://github.com/maxulysse))
 - [[#358](https://github.com/nf-core/differentialabundance/pull/358)] - Fixed nf-tests not running due to `--changed-since HEAD^`([@atrigila](https://github.com/atrigila), review by [@pinin4fjords](https://github.com/pinin4fjords))
 - [[#344](https://github.com/nf-core/differentialabundance/pull/344)] - Fixed replacement of NA sub-strings

assets/schema_contrasts.json

@@ -15,7 +15,7 @@
                     },
                     "formula": {
                         "type": "string",
-                        "pattern": "^~\\s*[a-zA-Z_][a-zA-Z0-9_]*(\\s*([:+*])\\s*[a-zA-Z_][a-zA-Z0-9_]*)*$"
+                        "pattern": "^~\\s*(?:[A-Za-z0-9_]+(?:\\s*(?:[:+*])\\s*[A-Za-z0-9_]+)*)?(?:\\s*-\\s*1)?$"
                     },
                     "comparison": {
                         "type": "array",

tests/assets/zero_intercept_contrasts.yml

@@ -0,0 +1,23 @@
+contrasts:
+  - id: treatment_effect_classic_comparison
+    comparison: ["treatment", "Control", "Treated"]
+
+  - id: treatment_plus_genotype
+    formula: "~ treatment + genotype"
+    make_contrasts_str: "treatmentTreated"
+
+  - id: interaction_genotype_treatment
+    formula: "~ genotype * treatment"
+    make_contrasts_str: "genotypeWT.treatmentTreated"
+
+  - id: full_model_with_interactions
+    formula: "~ genotype * treatment * time"
+    make_contrasts_str: "genotypeWT.treatmentTreated.time"
+
+  - id: zero_intercept_model_1
+    formula: "~ 0 + genotype"
+    make_contrasts_str: "genotypeWT"
+
+  - id: zero_intercept_model_2
+    formula: "~ genotype - 1"
+    make_contrasts_str: "genotypeWT"

tests/test_rnaseq_dream.nf.test

@@ -67,6 +67,35 @@ nextflow_pipeline {
         }
     }
 
+    test("Test rnaseq dream profile - complex contrast - with zero intercept") {
+        when {
+            params {
+                outdir        = "$outputDir"
+                contrasts_yml = "$projectDir/tests/assets/zero_intercept_contrasts.yml"
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_differentialabundance_software_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
+                ).match() }
+                )
+        }
+    }
+
     test("Test rnaseq dream profile - with decoupler") {
 
         when {

tests/test_rnaseq_dream.nf.test.snap

@@ -171,5 +171,59 @@
             "nextflow": "25.04.7"
         },
         "timestamp": "2025-09-23T15:46:34.43412188"
+    },
+    "Test rnaseq dream profile - complex contrast - with zero intercept": {
+        "content": [
+            14,
+            {
+                "CUSTOM_FILTERDIFFERENTIALTABLE": {
+                    "pandas": "1.5.2"
+                },
+                "GTF_TO_TABLE": {
+                    "atlas-gene-annotation-manipulation": "1.1.1"
+                },
+                "GUNZIP_GTF": {
+                    "gunzip": 1.1
+                },
+                "VALIDATOR": {
+                    "r-shinyngs": "2.2.4"
+                },
+                "VARIANCEPARTITION_DREAM": {
+                    "r-base": "4.3.3",
+                    "bioconductor-edger": "4.0.16",
+                    "variancePartition": "1.32.2"
+                },
+                "Workflow": {
+                    "nf-core/differentialabundance": "v1.6.0dev"
+                }
+            },
+            [
+                "pipeline_info",
+                "pipeline_info/collated_versions.yml",
+                "pipeline_info/nf_core_differentialabundance_software_versions.yml",
+                "tables",
+                "tables/annotation",
+                "tables/annotation/SRP254919.anno.tsv",
+                "tables/differential",
+                "tables/differential/full_model_with_interactions_SRP254919.dream.results.tsv",
+                "tables/differential/full_model_with_interactions_SRP254919.dream.results_filtered.tsv",
+                "tables/differential/interaction_genotype_treatment_SRP254919.dream.results.tsv",
+                "tables/differential/interaction_genotype_treatment_SRP254919.dream.results_filtered.tsv",
+                "tables/differential/treatment_plus_genotype_SRP254919.dream.results.tsv",
+                "tables/differential/treatment_plus_genotype_SRP254919.dream.results_filtered.tsv",
+                "tables/differential/zero_intercept_model_1_SRP254919.dream.results.tsv",
+                "tables/differential/zero_intercept_model_1_SRP254919.dream.results_filtered.tsv",
+                "tables/differential/zero_intercept_model_2_SRP254919.dream.results.tsv",
+                "tables/differential/zero_intercept_model_2_SRP254919.dream.results_filtered.tsv"
+            ],
+            [
+                "SRP254919.anno.tsv:md5,c1d7f21e64bd00f845ec6545c123a1fb"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.8"
+        },
+        "timestamp": "2025-10-07T12:38:36.288584939"
     }
 }