Update nextflow_schema.json

nf-core · May 15, 2024 · f4304ad · f4304ad
1 parent c95b11c
commit f4304ad
Showing 1 changed file with 21 additions and 6 deletions.
diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -315,6 +315,8 @@
             "properties": {
                 "cellranger_vdj_index": {
                     "type": "string",
+                    "format": "path",
+                    "exists": true,
                     "description": "Specify a pre-built cellranger index for VDJ analysis"
                 },
                 "skip_cellrangermulti_vdjref": {
@@ -323,31 +325,44 @@
                 },
                 "gex_frna_probe_set": {
                     "type": "string",
-                    "description": "TODO: Need help in defining a description for param."
+                    "format": "file-path",
+                    "exists": true,
+                    "description": "Provide a probe set for fixed RNA-seq profiling (used with FFPE samples)."
                 },
                 "gex_target_panel": {
                     "type": "string",
-                    "description": "TODO: Need help in defining a description for param."
+                    "description": "Provide a panel description for targeted sequencing.",
+                    "format": "file-path",
+                    "exists": "true"
                 },
                 "gex_cmo_set": {
                     "type": "string",
-                    "description": "TODO: Need help in defining a description for param."
+                    "format": "file-path",
+                    "exists": "true",
+                    "description": "Provide a Cell Multiplexing Oligo (CMO) description file when working with multiplexed samples."
                 },
                 "fb_reference": {
                     "type": "string",
-                    "description": "TODO: Need help in defining a description for param."
+                    "format": "file-path",
+                    "exists": true,
+                    "description": "Provide a reference file for feature barcoding (e.g. antibody measurements)."
                 },
                 "vdj_inner_enrichment_primers": {
                     "type": "string",
-                    "description": "TODO: Need help in defining a description for param."
+                    "description": "This argument takes a .txt file containing primer sequences that were used to enrich cDNA for V(D)J sequences.",
+                    "format": "file-path",
+                    "exists": true
                 },
                 "gex_barcode_sample_assignment": {
                     "type": "string",
                     "description": "TODO: Need help in defining a description for param."
                 },
                 "cellranger_multi_barcodes": {
                     "type": "string",
-                    "description": "TODO: Need help in defining a description for param."
+                    "format": "file-path",
+                    "exists": true,
+                    "mimetype": "text/csv",
+                    "description": "Additional samplesheet to provide information about multiplexed samples. See the 'Usage' section for more details."
                 }
             }
         },