Lima integration wip

suzannejin · Jul 3, 2024 · db4e959 · db4e959
1 parent 99142bd
commit db4e959
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Showing 4 changed files with 10 additions and 3 deletions.
diff --git a/modules/nf-core/limma/differential/main.nf b/modules/nf-core/limma/differential/main.nf
diff --git a/...e/limma/differential/templates/limma_de.R → ...erential/templates/limma_de_micro_array.R b/...e/limma/differential/templates/limma_de.R → ...erential/templates/limma_de_micro_array.R
diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -1314,7 +1314,7 @@
             "$ref": "#/definitions/deseq2_specific_options_rna_seq_only"
         },
         {
-            "$ref": "#/definitions/limma_specific_options_microarray_only"
+            "$ref": "#/definitions/limma_specific_options"
         },
         {
             "$ref": "#/definitions/gsea"

diff --git a/workflows/differentialabundance.nf b/workflows/differentialabundance.nf
@@ -346,7 +346,8 @@ workflow DIFFERENTIALABUNDANCE {
 
         LIMMA_DIFFERENTIAL (
             ch_contrasts,
-            ch_samples_and_matrix
+            ch_samples_and_matrix,
+            params.study_type
         )
         ch_differential = LIMMA_DIFFERENTIAL.out.results
         ch_model = LIMMA_DIFFERENTIAL.out.model