Add quantification_tools to nextflow_schema.json

nf-core · Sep 24, 2024 · 1e6b98d · 1e6b98d
1 parent 288f06a
commit 1e6b98d
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Showing 2 changed files with 9 additions and 1 deletion.
diff --git a/nextflow.config b/nextflow.config
@@ -22,7 +22,7 @@ params {
     tool_filter                = 1
     exon_boundary              = 0
     save_intermediates         = false
-    quantification_tools       = 'psirc,ciriquant'
+    quantification_tools       = 'ciriquant,psirc'
 
     // References
     genome                     = null

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -139,6 +139,14 @@
                     "help_text": "During annotation, if one of the start or end position of a circular candidate imperfectly overlaps an exon boundary, the script will consider positions within 'exon_boundary' (default 0bp) to be an exonic circRNA. If they fall outside of this range, the candidate is assumed to be an exonic-intronic circRNA, and the entire underlying sequence is taken for miRNA analysis, as opposed to just the exonic sequences for canonical exonic circRNAs. ",
                     "default": 0
                 },
+                "quantification_tools": {
+                    "type": "string",
+                    "fa_icon": "fas fa-wrench",
+                    "description": "Comma separated list of circRNA quantification tools to use. Supported tools: ciriquant, psirc",
+                    "help_text": "Select one or a combination of circRNA quantification tools for the pipeline e.g:\n--quantification_tools 'ciriquant,psirc'",
+                    "default": "ciriquant,psirc",
+                    "pattern": "^((ciriquant|psirc)(,(ciriquant|psirc))*)+$"
+                },
                 "mirna_tools": {
                     "type": "string",
                     "fa_icon": "fas fa-wrench",