test: set seed for formula test

Author: atrigila

conf/modules.config

@@ -267,6 +267,7 @@ process {
             "--vst_nsub $meta.params.deseq2_vst_nsub",
             "--shrink_lfc $meta.params.deseq2_shrink_lfc",
             "--cores $meta.params.deseq2_cores",
+            "--seed $meta.params.deseq2_seed",
             "--subset_to_contrast_samples $meta.params.differential_subset_to_contrast_samples",
             ((meta.params.round_digits != null && meta.params.round_digits > 0) ? "--round_digits $meta.params.round_digits" : ""),
             ((meta.blocking == null) ? '' : "--blocking_variables $meta.blocking")

nextflow.config

@@ -119,6 +119,7 @@ params {
     deseq2_cores                      = 1
     deseq2_vs_blind                   = true
     deseq2_vst_nsub                   = 1000
+    deseq2_seed                       = null
 
     // Limma-specific options
     limma_ndups             = null

nextflow_schema.json

@@ -699,6 +699,10 @@
                     "help_text": "Number of cores to use with DESeq()",
                     "fa_icon": "fab fa-centercode"
                 },
+                "deseq2_seed": {
+                    "type": "integer",
+                    "fa_icon": "fas fa-seedling"
+                },
                 "deseq2_vs_blind": {
                     "type": "boolean",
                     "default": true,

tests/default.nf.test

@@ -111,6 +111,7 @@ nextflow_pipeline {
                 exploratory_log2_assays = "raw"
                 skip_reports        = true
                 transcript_length_matrix = null
+                deseq2_seed         = 1
 
             }
         }