Surface v0.5 submission fields in MultiQC plugin

docs/adoption-plan.md

@@ -42,6 +42,8 @@ Goal: make FastaGuard visible in standard pipeline reports.
 - Continue emitting `fastaguard_mqc.json` custom content.
 - Develop `integrations/multiqc/` into a packaged MultiQC plugin.
 - Test the plugin against multiple sample reports.
+- Keep v0.5 gate, readiness, and submission fields visible in the native
+  MultiQC summary table.
 - Decide whether to submit upstream to MultiQC once public adoption begins.
 
 Done when:

docs/packaging.md

@@ -183,4 +183,4 @@ cd ../../examples/reports
 multiqc .
 ```
 
-This is intentionally compact: it parses `fastaguard_mqc.json`, adds key metrics to MultiQC general stats, and adds a FastaGuard summary section. The full evidence remains in FastaGuard's own HTML and JSON reports.
+This is intentionally compact: it parses `fastaguard_mqc.json`, adds key metrics to MultiQC general stats, and adds a FastaGuard summary section with gate, readiness, and submission-readiness fields. The full evidence remains in FastaGuard's own HTML and JSON reports.

integrations/multiqc/README.md

@@ -3,8 +3,9 @@
 This directory contains a dedicated MultiQC plugin starter for FastaGuard.
 
 FastaGuard already emits MultiQC custom-content JSON as `fastaguard_mqc.json`.
-This plugin is the next step: a native module that can add FastaGuard verdicts
-and key assembly preflight metrics directly to MultiQC reports.
+This plugin is the next step: a native module that can add FastaGuard verdicts,
+gate status, readiness status, submission readiness, and key assembly preflight
+metrics directly to MultiQC reports.
 
 ## Local Install
 
@@ -42,7 +43,10 @@ multiqc --strict --module fastaguard examples/reports
 
 - Parse FastaGuard custom-content JSON.
 - Add verdict and summary metrics to the MultiQC general stats table.
-- Add one FastaGuard summary table section.
+- Add one FastaGuard summary table section with gate, readiness, and v0.5
+  submission fields including `submission_target`, `submission_status`,
+  unsafe identifier counts, long identifier counts, duplicate first-token ID
+  counts, and gap-like N-run counts.
 
 Keep the module compact. MultiQC should summarize many FastaGuard reports, not
 replicate every field from the full FastaGuard HTML report.

integrations/multiqc/src/fastaguard_multiqc/multiqc_module.py

@@ -204,6 +204,38 @@ def _summary_headers() -> dict:
                 "title": "Readiness blockers",
                 "description": "Readiness categories and finding IDs blocking downstream use",
             },
+            "submission_target": {
+                "title": "Submission target",
+                "description": "Submission target profile used by FastaGuard",
+            },
+            "submission_status": {
+                "title": "Submission status",
+                "description": "FASTA-level submission readiness status",
+            },
+            "unsafe_identifier_count": {
+                "title": "Unsafe IDs",
+                "description": "Number of identifiers with submission-unsafe characters",
+                "min": 0,
+                "scale": "OrRd",
+            },
+            "long_identifier_count": {
+                "title": "Long IDs",
+                "description": "Number of identifiers longer than the submission advisory threshold",
+                "min": 0,
+                "scale": "YlOrBr",
+            },
+            "duplicate_first_token_id_count": {
+                "title": "Duplicate first-token IDs",
+                "description": "Number of duplicate first-token FASTA identifiers",
+                "min": 0,
+                "scale": "OrRd",
+            },
+            "gap_like_n_run_count": {
+                "title": "Gap-like N runs",
+                "description": "Number of records with gap-like N runs worth submission review",
+                "min": 0,
+                "scale": "YlOrBr",
+            },
             "duplicate_id_count": {
                 "title": "Duplicate IDs",
                 "description": "Number of duplicate FASTA record IDs",

integrations/multiqc/src/fastaguard_multiqc/parser.py

@@ -24,6 +24,12 @@
     "gate_blocking_findings",
     "readiness_status",
     "readiness_blockers",
+    "submission_target",
+    "submission_status",
+    "unsafe_identifier_count",
+    "long_identifier_count",
+    "duplicate_first_token_id_count",
+    "gap_like_n_run_count",
     "duplicate_id_count",
     "invalid_sequence_count",
     "high_n_sequence_count",

tests/python/test_adoption_assets.py

@@ -155,6 +155,9 @@ def test_multiqc_parser_reads_fastaguard_custom_content(self):
         self.assertEqual(summary["valid_assembly"]["gate_status"], "WARN")
         self.assertEqual(summary["valid_assembly"]["readiness_status"], "WARN")
         self.assertEqual(summary["valid_assembly"]["readiness_blockers"], "")
+        self.assertEqual(summary["valid_assembly"]["submission_target"], ".")
+        self.assertEqual(summary["valid_assembly"]["submission_status"], "WARN")
+        self.assertEqual(summary["valid_assembly"]["duplicate_first_token_id_count"], 0)
         self.assertEqual(summary["valid_assembly"]["sequence_count"], 3)
         self.assertEqual(summary["valid_assembly"]["n50"], 16)
 
@@ -172,6 +175,12 @@ def test_multiqc_parser_reads_expanded_fields_from_cli_example(self):
                 "gate_blocking_findings": "duplicate_ids,duplicate_first_token_ids,invalid_chars",
                 "readiness_status": "FAIL",
                 "readiness_blockers": "index.duplicate_ids,submission.duplicate_ids,index.duplicate_first_token_ids,submission.duplicate_first_token_ids,alphabet.invalid_chars,submission.invalid_chars",
+                "submission_target": ".",
+                "submission_status": "FAIL",
+                "unsafe_identifier_count": 0,
+                "long_identifier_count": 0,
+                "duplicate_first_token_id_count": 1,
+                "gap_like_n_run_count": 0,
                 "sequence_count": 5,
                 "total_length": 145,
                 "n50": 110,
@@ -221,6 +230,12 @@ def test_multiqc_parser_reads_expanded_summary_fields(self):
                                 "finding_count": 4,
                                 "readiness_status": "WARN",
                                 "readiness_blockers": "assembly.high_n_rate",
+                                "submission_target": "ncbi",
+                                "submission_status": "WARN",
+                                "unsafe_identifier_count": 1,
+                                "long_identifier_count": 1,
+                                "duplicate_first_token_id_count": 2,
+                                "gap_like_n_run_count": 3,
                             }
                         },
                     }
@@ -240,6 +255,10 @@ def test_multiqc_parser_reads_expanded_summary_fields(self):
                     "n_percent": 2.5,
                     "finding_count": 4,
                     "duplicate_id_count": 1,
+                    "unsafe_identifier_count": 1,
+                    "long_identifier_count": 1,
+                    "duplicate_first_token_id_count": 2,
+                    "gap_like_n_run_count": 3,
                     "invalid_sequence_count": 0,
                     "high_n_sequence_count": 2,
                     "tiny_contig_count": 1,
@@ -249,6 +268,8 @@ def test_multiqc_parser_reads_expanded_summary_fields(self):
                     "composite_anomaly_count": 1,
                     "readiness_status": "WARN",
                     "readiness_blockers": "assembly.high_n_rate",
+                    "submission_target": "ncbi",
+                    "submission_status": "WARN",
                 },
             )
 
@@ -400,8 +421,23 @@ def test_multiqc_plugin_summary_headers_include_gate_fields(self):
         self.assertIn('"gate_blocking_findings"', module_source)
         self.assertIn('"readiness_status"', module_source)
         self.assertIn('"readiness_blockers"', module_source)
+        self.assertIn('"submission_target"', module_source)
+        self.assertIn('"submission_status"', module_source)
+        self.assertIn('"unsafe_identifier_count"', module_source)
+        self.assertIn('"long_identifier_count"', module_source)
+        self.assertIn('"duplicate_first_token_id_count"', module_source)
+        self.assertIn('"gap_like_n_run_count"', module_source)
         self.assertIn("Finding IDs blocking the FastaGuard gate", module_source)
         self.assertIn("FastaGuard readiness status", module_source)
+        self.assertIn("FASTA-level submission readiness status", module_source)
+
+    def test_multiqc_docs_describe_submission_fields(self):
+        readme = (ROOT / "integrations" / "multiqc" / "README.md").read_text()
+
+        self.assertIn("submission readiness", readme)
+        self.assertIn("`submission_target`", readme)
+        self.assertIn("`submission_status`", readme)
+        self.assertIn("duplicate first-token", readme)
 
     def test_multiqc_plugin_registers_filename_first_fastaguard_search_pattern(self):
         patterns = getattr(multiqc_parser, "FASTAGUARD_SEARCH_PATTERN", {})