solve issue with dream test

Author: suzannejin

conf/test_rnaseq_dream.config

@@ -19,10 +19,9 @@ params {
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
     // Input data
-    input                    = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.csv'
-    matrix                   = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv'
-    transcript_length_matrix = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.spoofed_lengths.tsv'
-    contrasts_yml            = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/differentialabundance/testdata/formula_contrasts/SRP254919.contrasts.yaml'
+    input               = 'https://github.com/nf-core/test-datasets/raw/differentialabundance/modules_testdata/variancepartition_dream/metadata.tsv'
+    matrix              = 'https://github.com/nf-core/test-datasets/raw/differentialabundance/modules_testdata/variancepartition_dream/counts.tsv'
+    contrasts_yml       = 'https://github.com/nf-core/test-datasets/raw/differentialabundance/testdata/formula_contrasts/rnaseq_complex_contrast.yaml'
 
     // To do: replace this with a cut-down mouse GTF matching the matrix for testing
     gtf = 'https://ftp.ensembl.org/pub/release-81/gtf/mus_musculus/Mus_musculus.GRCm38.81.gtf.gz'
@@ -51,14 +50,6 @@ params {
     exploratory_log2_assays   = 'raw,normalised'
     exploratory_main_variable = 'contrasts'
 
-    // Test dataset is too small for the nsub default value
-    deseq2_vst_nsub = 500
-
-    // Activate GSEA
-    functional_method = 'gsea'
-    gene_sets_files   = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/gene_set_analysis/mh.all.v2022.1.Mm.symbols.gmt'
-    gsea_rnd_seed     = '10'
-
     // Report options
     report_contributors = 'Jane Doe\nDirector of Institute of Microbiology\nUniversity of Smallville;John Smith\nPhD student\nInstitute of Microbiology\nUniversity of Smallville'
 

tests/test_rnaseq_dream.nf.test

@@ -10,9 +10,10 @@ nextflow_pipeline {
 
         when {
             params {
-                outdir            = "$outputDir"
-                paramset_name     = "dream_rnaseq_gsea"
-                functional_method = null
+                outdir              = "$outputDir"
+                paramset_name       = "dream_rnaseq_gsea"
+                differential_method = null
+                functional_method   = null
             }
         }
 
@@ -42,10 +43,6 @@ nextflow_pipeline {
         when {
             params {
                 outdir        = "$outputDir"
-                    input                    = 'https://github.com/nf-core/test-datasets/raw/differentialabundance/modules_testdata/variancepartition_dream/metadata.tsv'
-                    matrix                   = 'https://github.com/nf-core/test-datasets/raw/differentialabundance/modules_testdata/variancepartition_dream/counts.tsv'
-                    contrasts_yml            = 'https://github.com/nf-core/test-datasets/raw/differentialabundance/testdata/formula_contrasts/rnaseq_complex_contrast.yaml'
-
             }
         }