Add nonpareil to testing

nf-core · Jun 11, 2024 · 6b47739 · 6b47739
1 parent 88d2b23
commit 6b47739
Showing 1 changed file with 28 additions and 27 deletions.
diff --git a/conf/test.config b/conf/test.config
@@ -20,33 +20,34 @@ params {
     max_time   = '6.h'
 
     // Input data
-    input                                 = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv'
-    databases                             = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.1.csv'
-    perform_shortread_qc                  = true
-    perform_longread_qc                   = true
-    shortread_qc_mergepairs               = true
-    perform_shortread_complexityfilter    = true
-    perform_shortread_hostremoval         = true
-    perform_longread_hostremoval          = true
-    perform_runmerging                    = true
-    hostremoval_reference                 = params.pipelines_testdata_base_path + 'modules/data/genomics/homo_sapiens/genome/genome.fasta'
-    run_kaiju                             = true
-    run_kraken2                           = true
-    run_bracken                           = true
-    run_malt                              = false
-    run_metaphlan                         = true
-    run_centrifuge                        = true
-    run_diamond                           = true
-    run_krakenuniq                        = true
-    run_motus                             = false
-    run_ganon                             = true
-    run_krona                             = true
-    run_kmcp                              = true
-    krona_taxonomy_directory              = params.pipelines_testdata_base_path + 'modules/data/genomics/sarscov2/metagenome/krona_taxonomy.tab'
-    malt_save_reads                       = true
-    kraken2_save_reads                    = true
-    centrifuge_save_reads                 = true
-    run_profile_standardisation           = true
+    input                                  = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv'
+    databases                              = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.1.csv'
+    perform_shortread_qc                   = true
+    perform_shortread_redundancyestimation = true
+    perform_longread_qc                    = true
+    shortread_qc_mergepairs                = true
+    perform_shortread_complexityfilter     = true
+    perform_shortread_hostremoval          = true
+    perform_longread_hostremoval           = true
+    perform_runmerging                     = true
+    hostremoval_reference                  = params.pipelines_testdata_base_path + 'modules/data/genomics/homo_sapiens/genome/genome.fasta'
+    run_kaiju                              = true
+    run_kraken2                            = true
+    run_bracken                            = true
+    run_malt                               = false
+    run_metaphlan                          = true
+    run_centrifuge                         = true
+    run_diamond                            = true
+    run_krakenuniq                         = true
+    run_motus                              = false
+    run_ganon                              = true
+    run_krona                              = true
+    run_kmcp                               = true
+    krona_taxonomy_directory               = params.pipelines_testdata_base_path + 'modules/data/genomics/sarscov2/metagenome/krona_taxonomy.tab'
+    malt_save_reads                        = true
+    kraken2_save_reads                     = true
+    centrifuge_save_reads                  = true
+    run_profile_standardisation            = true
 }
 
 process {