From 287916e58ce3f61a5a5aa075764d819de45aa455 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Fri, 27 Sep 2024 13:38:52 +1200 Subject: [PATCH] Updated input schema and stub test --- assets/schema_input.json | 4 ++-- tests/stub/assemblysheet.csv | 6 +++--- tests/stub/benchmark/red5_v3.benchmark.gff3 | 0 3 files changed, 5 insertions(+), 5 deletions(-) create mode 100644 tests/stub/benchmark/red5_v3.benchmark.gff3 diff --git a/assets/schema_input.json b/assets/schema_input.json index 86627ea..0824476 100644 --- 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 index 10581ff..07e072b 100644 --- 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 new file mode 100644 index 0000000..e69de29