diff --git a/nextflow_schema.json b/nextflow_schema.json index c2537df0..acc13051 100644 --- 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": { @@ -323,23 +325,33 @@ }, "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", @@ -347,7 +359,10 @@ }, "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." } } },