updated schema

phac-nml · Dec 11, 2023 · d7fbcfb · d7fbcfb
1 parent 07cf9db
commit d7fbcfb
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Showing 2 changed files with 7 additions and 2 deletions.
diff --git a/nextflow.config b/nextflow.config
@@ -271,7 +271,7 @@ params {
         report_ext = ".tsv"
         report_tag = "QUAST"
         min_contig_length = 1000
-        quast_contigs_field = "# contigs"
+        contigs_field = "# contigs"
         // need to add a --min-contig args to set to 0 as at 500 currently add --report-all-metrics
         // also need to see if a sam can be published from quast
         args = { "--min-contig ${params.quast.min_contig_length} --report-all-metrics" }
@@ -841,7 +841,7 @@ params {
             high_msg = "N50 value is high, this is likely a good thing if you have fewer contigs than expected."
         }
         nr_contigs {
-            path = [params.quast.report_tag, "0", params.quas.quast_contigs_field]
+            path = [params.quast.report_tag, "0", params.quast.contigs_field]
             coerce_type = 'Integer'
             compare_fields = ['min_nr_contigs', 'max_nr_contigs']
             comp_type = "range"

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -1890,6 +1890,11 @@
                     "type": "string",
                     "default": "--min-contig 0 --report-all-metrics",
                     "hidden": true
+                },
+                "quast.contigs_field": {
+                    "type": "string",
+                    "default": "# contigs",
+                    "hidden": true
                 }
             }
         },