Updated input schema and stub test

Plant-Food-Research-Open · Sep 27, 2024 · 287916e · 287916e
1 parent 3eb9ace
commit 287916e
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Showing 3 changed files with 5 additions and 5 deletions.
diff --git a/assets/schema_input.json b/assets/schema_input.json
@@ -68,14 +68,14 @@
                 "anyOf": [
                     {
                         "type": "string",
-                        "pattern": "^\\S+\\.gff(3)?(\\.gz)?$"
+                        "pattern": "^\\S+\\.gff(3)?$"
                     },
                     {
                         "type": "string",
                         "maxLength": 0
                     }
                 ],
-                "errorMessage": "GFF/GFF3 file for benchmarking cannot contain spaces and must have extension '.gff.gz', '.gff3.gz', '.gff' or '.gff3'"
+                "errorMessage": "GFF/GFF3 file for benchmarking cannot contain spaces and must have extension '.gff' or '.gff3'"
             }
         },
         "required": ["tag", "fasta", "is_masked"]

diff --git a/tests/stub/assemblysheet.csv b/tests/stub/assemblysheet.csv
@@ -1,5 +1,5 @@
-tag,fasta,is_masked,te_lib,braker_gff3,braker_hints
-red5_v2p1,tests/stub/assembly/red5_v2p1_chr1.fasta.gz,no,,tests/stub/braker/red5_v2p1.gff3.gz,tests/stub/braker/red5_v2p1.hints.gff.gz
+tag,fasta,is_masked,te_lib,braker_gff3,braker_hints,benchmark
+red5_v2p1,tests/stub/assembly/red5_v2p1_chr1.fasta.gz,no,,tests/stub/braker/red5_v2p1.gff3.gz,tests/stub/braker/red5_v2p1.hints.gff.gz,
 donghong,tests/stub/assembly/donghong.chr1.fsa.gz,no,tests/stub/te_lib/donghong.TElib.fa.gz,tests/stub/braker/red5_v2p1.gff3.gz,tests/stub/braker/red5_v2p1.hints.gff.gz
-red5_v3,tests/stub/assembly/red5_v3_chr1.fasta,yes
+red5_v3,tests/stub/assembly/red5_v3_chr1.fasta,yes,,,,tests/stub/benchmark/red5_v3.benchmark.gff3
 red7_v5,tests/stub/assembly/red7_v5_chr3.fasta,no
diff --git a/tests/stub/benchmark/red5_v3.benchmark.gff3 b/tests/stub/benchmark/red5_v3.benchmark.gff3