From bdbe5371b18f9150217e83772f28d6757f92a6ae Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Fri, 25 Oct 2024 14:53:05 +0200
Subject: [PATCH] Migrate to nf-validation

---
 assets/schema_fasta.json | 15 +++++++++------
 assets/schema_input.json | 22 +++++++++++++---------
 2 files changed, 22 insertions(+), 15 deletions(-)

diff --git a/assets/schema_fasta.json b/assets/schema_fasta.json
index 54e00de8e..c6a13f8f6 100644
--- a/assets/schema_fasta.json
+++ b/assets/schema_fasta.json
@@ -11,7 +11,6 @@
                 "type": "string",
                 "pattern": "^\\S+$",
                 "meta": ["id"],
-                "unique": true,
                 "errorMessage": "Reference name must be provided and cannot contain spaces."
             },
             "fasta": {
@@ -19,7 +18,6 @@
                 "format": "file-path",
                 "pattern": "^\\S+\\.f(na|asta|a|as)(\\.gz)?$",
                 "exists": true,
-                "unique": true,
                 "errorMessage": "Fasta files for the mapping reference must be provided with file extensions '.fasta', '.fa', '.fas', '.fna', '.fasta.gz','.fa.gz','.fas.gz', '.fna.gz' and cannot contain any spaces."
             },
             "fai": {
@@ -79,7 +77,6 @@
                 "format": "file-path",
                 "pattern": "^\\S+\\.bed(\\.gz)?$",
                 "exists": true,
-                "dependentRequired": ["pileupcaller_snpfile"],
                 "errorMessage": "SNP capture bed files for pileupcaller must not contain any spaces, have file extensions '.bed' or '.bed.gz' and be provided alongside a pileupcall_bedfile."
             },
             "pileupcaller_snpfile": {
@@ -87,7 +84,6 @@
                 "format": "file-path",
                 "pattern": "^\\S+\\.snp$",
                 "exists": true,
-                "dependentRequired": ["pileupcaller_bedfile"],
                 "errorMessage": "SNP panel files for pileupcaller must not contain any spaces, have file extension '.snp' and be provided alongside a pileupcaller_snpfile."
             },
             "hapmap_file": {
@@ -138,6 +134,13 @@
                 "errorMessage": "SNP annotation files for GATK must not contain any spaces and have file extension '.vcf'."
             }
         },
-        "required": ["reference_name", "fasta"]
-    }
+        "required": ["reference_name", "fasta"],
+        "dependentRequired": {
+            "pileupcaller_snpfile": ["pileupcaller_bedfile"],
+            "pileupcaller_bedfile": ["pileupcaller_snpfile"],
+            "bam": ["bam_reference_id"],
+            "bam_reference_id": ["bam"]
+        }
+    },
+    "allOf": [{ "uniqueEntries": "reference_name" }, { "uniqueEntries": "fasta" }]
 }
diff --git a/assets/schema_input.json b/assets/schema_input.json
index 7956b0f09..673a694a2 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -21,7 +21,6 @@
             },
             "lane": {
                 "type": "integer",
-                "unique": ["library_id"],
                 "meta": ["lane"],
                 "errorMessage": "Sequencing lane number must be provided and specified as an integer. If no lane information, specify 0."
             },
@@ -54,7 +53,6 @@
                 "format": "file-path",
                 "pattern": "^\\S+\\.f(ast)?q\\.gz$",
                 "exists": true,
-                "unique": true,
                 "errorMessage": "FastQ file for reads 1 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'."
             },
             "r2": {
@@ -62,8 +60,6 @@
                 "format": "file-path",
                 "pattern": "^\\S+\\.f(ast)?q\\.gz$",
                 "exists": true,
-                "unique": true,
-                "dependentRequired": ["r1"],
                 "errorMessage": "FastQ file for reads 2 require files for reads 1, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'."
             },
             "bam": {
@@ -71,14 +67,11 @@
                 "format": "file-path",
                 "pattern": "^\\S+\\.bam$",
                 "exists": true,
-                "unique": true,
-                "dependentRequired": ["bam_reference_id"],
                 "errorMessage": "BAM files cannot contain any spaces and must have extension '.bam'."
             },
             "bam_reference_id": {
                 "type": "string",
                 "meta": ["bam_reference_id"],
-                "dependentRequired": ["bam"],
                 "errorMessage": "A BAM reference ID (corresponding to what is supplied to `--fasta`) must always be provided when providing a BAM file."
             }
         },
@@ -98,6 +91,17 @@
             {
                 "required": ["bam"]
             }
-        ]
-    }
+        ],
+        "dependentRequired": {
+            "r2": ["r1"],
+            "bam": ["bam_reference_id"],
+            "bam_reference_id": ["bam"]
+        }
+    },
+    "allOf": [
+        { "uniqueEntries": ["lane", "library_id"] },
+        { "uniqueEntries": "r1" },
+        { "uniqueEntries": "r2" },
+        { "uniqueEntries": "bam" }
+    ]
 }