From c55a854345b1d2f1b8f3f4dbd5a09e9fb5e2a122 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Wed, 18 Oct 2023 21:45:52 -0500
Subject: [PATCH] feat: Add input schema

---
 assets/schema_input.json | 23 +++++++++++++++++++++++
 nextflow_schema.json     |  3 +--
 2 files changed, 24 insertions(+), 2 deletions(-)
 create mode 100644 assets/schema_input.json

diff --git a/assets/schema_input.json b/assets/schema_input.json
new file mode 100644
index 0000000..80cf68b
--- /dev/null
+++ b/assets/schema_input.json
@@ -0,0 +1,23 @@
+{
+  "$schema": "http://json-schema.org/draft-07/schema",
+  "$id": "https://raw.githubusercontent.com/nf-core/taxprofiler/master/assets/schema_input.json",
+  "title": "haplotyper battle royale pipeline - params.input schema",
+  "description": "Schema for the file provided with params.input",
+  "type": "array",
+  "items": {
+    "type": "object",
+    "properties": {
+      "sample": {
+        "type": "string",
+        "pattern": "^\\S+$",
+        "errorMessage": "Sample name must be provided and cannot contain spaces"
+      },
+      "fastq_1": {
+        "type": "string",
+        "pattern": "^\\S+\\.f(ast)?q\\.gz$",
+        "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
+      }
+    },
+    "required": ["sample", "fastq_1"]
+  }
+}
diff --git a/nextflow_schema.json b/nextflow_schema.json
index d4c5c27..9871a3d 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -25,8 +25,7 @@
         "reference": {
           "type": "string",
           "fa_icon": "fas fa-dna",
-          "description": "NCBI accession number of the reference genome to align reads against",
-          "pattern": "^[:upper:]{2}_[:digit:]{6}\\.[:digit:]+$"
+          "description": "NCBI accession number of the reference genome to align reads against"
         },
         "outdir": {
           "type": "string",