update test_affy

Author: SusiJo

tests/test_affy.nf.test.bak tests/test_affy.nf.testtests/test_affy.nf.test.bak renamed to tests/test_affy.nf.test

@@ -14,30 +14,6 @@ nextflow_pipeline {
             params {
                 outdir                     = "$outputDir"
                 study_name                 = 'GSE50790'
-                config_profile_name        = 'Affy array test profile'
-                config_profile_description = 'Minimal test dataset to check pipeline function'
-
-                // Input data
-                input                  = 'https://raw.githubusercontent.com/nf-core/test-datasets/differentialabundance/testdata/GSE50790.csv'
-                contrasts_yml          = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/differentialabundance/testdata/GSE50790_contrasts.yaml'
-                affy_cel_files_archive = 'https://raw.githubusercontent.com/nf-core/test-datasets/differentialabundance/testdata/GSE50790_RAW.tar'
-
-                // Observations
-                observations_id_col   = 'name'
-                observations_name_col = 'name'
-
-                // Exploratory
-                exploratory_main_variable = 'contrasts'
-
-                // Differential
-                differential_max_pval        = 0.05
-                differential_max_qval        = 0.05
-                differential_min_fold_change = 1.5
-
-                // Activate GSEA
-                functional_method = 'gsea'
-                gene_sets_files   = 'https://raw.githubusercontent.com/nf-core/test-datasets/differentialabundance/testdata/h.all.v2022.1.Hs.symbols.gmt'
-                gsea_rnd_seed     = '10'
 
             }
         }
@@ -56,6 +32,7 @@ nextflow_pipeline {
                     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("$outputDir/pipeline_info/collated_versions.yml"),
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_differentialabundance_software_versions.yml"),
                     // All stable path name, with a relative path
                     stable_name,
                     // All files with stable contents
@@ -73,31 +50,6 @@ nextflow_pipeline {
                 paramset_name       = "limma_affy_gsea"
                 differential_method = null
                 functional_method   = null
-
-                study_name                 = 'GSE50790'
-                config_profile_name        = 'Affy array test profile'
-                config_profile_description = 'Minimal test dataset to check pipeline function'
-
-                // Input data
-                input                  = 'https://raw.githubusercontent.com/nf-core/test-datasets/differentialabundance/testdata/GSE50790.csv'
-                contrasts_yml          = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/differentialabundance/testdata/GSE50790_contrasts.yaml'
-                affy_cel_files_archive = 'https://raw.githubusercontent.com/nf-core/test-datasets/differentialabundance/testdata/GSE50790_RAW.tar'
-
-                // Observations
-                observations_id_col   = 'name'
-                observations_name_col = 'name'
-
-                // Exploratory
-                exploratory_main_variable = 'contrasts'
-
-                // Differential
-                differential_max_pval        = 0.05
-                differential_max_qval        = 0.05
-                differential_min_fold_change = 1.5
-
-                // Activate GSEA
-                gene_sets_files   = 'https://raw.githubusercontent.com/nf-core/test-datasets/differentialabundance/testdata/h.all.v2022.1.Hs.symbols.gmt'
-                gsea_rnd_seed     = '10'
             }
         }
 
@@ -115,6 +67,7 @@ nextflow_pipeline {
                     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("$outputDir/pipeline_info/collated_versions.yml"),
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_differentialabundance_software_versions.yml"),
                     // All stable path name, with a relative path
                     stable_name,
                     // All files with stable contents