PR to fix issue 90 (Pipeline fails when test.fa missing)

nextflow.config

@@ -14,9 +14,9 @@ params {
     // Input options
     input                     = null // location for the input samplesheet file
     classifier                = "kraken2"
-    fasta                     = "test.fa"
+    fasta                     = null
     schema_ignore_params      = "fasta"
-    tracedir                  = "null"
+    tracedir                  = null
 
     //rasusa subsampling options
     skip_subsampling           = true
@@ -33,13 +33,13 @@ params {
     skip_seqqc                = false
     skip_trimming             = false
     trim_tool                 = "fastp"  // Select which trimming tool to use (fastp/trimmomatic/trimgalore)
-    adapter_fasta             = "/mnt/cidgoh-object-storage/database/adaptors/test.fa" // location for adapator database (fasta file)
+    adapter_fasta             = "" // location for adapator database (fasta file)
     save_trimmed_fail         = false //  Check if reads failed in the trimming process need to be saved (True/False, default: False)
     save_merged               = true  // Check if merged reads need to be saved (True/False, default: True)
 
 
     // MultiQC options
-    max_multiqc_email_size     = '25.MB'
+    max_multiqc_email_size     = "25.MB"
     multiqc_title              = "BACPAQ"
     multiqc_config             = null
     multiqc_logo               = null
@@ -144,7 +144,6 @@ params {
     version                    = false
     validate_params            = false
     show_hidden_params         = false
-    schema_ignore_params       = 'genomes'
 
     // assembly QC options
     skip_checkm                = false

nextflow_schema.json

@@ -38,7 +38,7 @@
         },
         "fasta": {
           "type": "string",
-          "default": "test.fa",
+          "default": "",
           "hidden": true,
           "format": "file-path",
           "mimetype": "fasta"