Merge branch 'CW-7271_missing_summary' into 'dev'

Add the missing annotation ref summary [CW-7271]

Closes CW-7271

See merge request epi2melabs/workflows/wf-transcriptomes!290

bin/workflow_glue/report.py

@@ -220,6 +220,17 @@ def _load_bambu_qc(bambu_dir):
     return None
 
 
+def _load_annotation_reference_summary(summary_file):
+    """Load reference/annotation preparation summary JSON from a file path."""
+    if summary_file is None:
+        return None
+    summary_path = Path(summary_file)
+    if summary_path.exists():
+        with open(summary_path) as f:
+            return json.load(f)
+    return None
+
+
 def _load_de_qc(de_dir):
     """Load DE/DTU QC statistics JSON."""
     qc_file = Path(de_dir) / "de_qc_stats.json"
@@ -229,15 +240,6 @@ def _load_de_qc(de_dir):
     return None
 
 
-def _load_annotation_reference_summary(cohort_dir):
-    """Load reference/annotation preparation summary JSON."""
-    summary_file = Path(cohort_dir) / "reference" / "annotation_reference_summary.json"
-    if summary_file.exists():
-        with open(summary_file) as f:
-            return json.load(f)
-    return None
-
-
 def _load_cpm_tables(cohort_dir):
     """Load cohort-level gene and transcript CPM tables."""
     cohort_dir = Path(cohort_dir)
@@ -478,8 +480,7 @@ def main(args):
                     .rename(columns={"index": "Field"}),
                     use_index=False,
                 )
-
-    annotation_reference_summary = _load_annotation_reference_summary(args.cohort_dir)
+    annotation_reference_summary = _load_annotation_reference_summary(args.ref_summary)
 
     if annotation_reference_summary:
         with report.add_section("Reference and Annotation Checks", "Reference"):
@@ -1210,6 +1211,11 @@ def argparser():
         default=None,
         help="Differential analysis directory.",
     )
+    parser.add_argument(
+        "--ref_summary",
+        default=None,
+        help="Annotation reference summary TSV.",
+    )
     parser.add_argument("--versions", required=True, help="Versions directory.")
     parser.add_argument("--params", required=True, help="Workflow params JSON.")
     parser.add_argument(

bin/workflow_glue/tests/common/test_report.py

@@ -145,6 +145,8 @@ def _build_report_args(tmp_path, de_qc=None):
         str(alignment_stats),
         "--cohort_dir",
         str(cohort),
+        "--ref_summary",
+        str(reference / "annotation_reference_summary.json"),
         "--samples_dir",
         str(samples),
         "--sqanti_dir",
@@ -229,6 +231,8 @@ def test_report_main_accepts_optional_file_sentinels(monkeypatch, tmp_path):
             str(alignment_stats),
             "--cohort_dir",
             str(cohort),
+            "--ref_summary",
+            str(cohort / "reference" / "annotation_reference_summary.json"),
             "--samples_dir",
             str(samples),
             "--sqanti_dir",
@@ -351,6 +355,8 @@ def test_report_main_handles_degenerate_bambu_qc_and_read_summary(
             str(alignment_stats),
             "--cohort_dir",
             str(cohort),
+            "--ref_summary",
+            str(cohort / "reference" / "annotation_reference_summary.json"),
             "--samples_dir",
             str(samples),
             "--sqanti_dir",
@@ -411,6 +417,24 @@ def test_report_main_uses_cohort_bambu_qc_for_multi_sample_inputs(
 
     cohort = tmp_path / "cohort"
     cohort.mkdir()
+    reference = cohort / "reference"
+    reference.mkdir()
+    _write(
+        reference / "annotation_reference_summary.json",
+        json.dumps(
+            {
+                "seqname_overlap": ["chr1"],
+                "only_in_annotation": [],
+                "only_in_reference": [],
+                "annotation": {
+                    "kept_records": 10,
+                    "excluded_unstranded_records": 0,
+                    "sanitised_attribute_records": 0,
+                },
+                "warnings": [],
+            }
+        ),
+    )
     _write(
         cohort / "bambu_qc_stats.json",
         json.dumps(
@@ -478,6 +502,8 @@ def test_report_main_uses_cohort_bambu_qc_for_multi_sample_inputs(
             str(alignment_stats),
             "--cohort_dir",
             str(cohort),
+            "--ref_summary",
+            str(cohort / "reference" / "annotation_reference_summary.json"),
             "--samples_dir",
             str(samples),
             "--sqanti_dir",

bin/workflow_glue/tests/common/test_report_qc.py

@@ -93,7 +93,9 @@ def test_load_annotation_reference_summary_exists(tmp_path):
     with open(summary_dir / "annotation_reference_summary.json", "w") as f:
         json.dump(summary_data, f)
 
-    result = _load_annotation_reference_summary(tmp_path / "cohort")
+    result = _load_annotation_reference_summary(
+        summary_dir / "annotation_reference_summary.json"
+    )
     assert result is not None
     assert result["seqname_overlap"] == ["chr1"]
     assert result["only_in_annotation"] == ["chrMissing"]
@@ -106,7 +108,9 @@ def test_load_annotation_reference_summary_missing(tmp_path):
     cohort_dir = tmp_path / "cohort"
     cohort_dir.mkdir()
 
-    result = _load_annotation_reference_summary(cohort_dir)
+    result = _load_annotation_reference_summary(
+        cohort_dir / "reference" / "annotation_reference_summary.json"
+    )
     assert result is None
 
 

main.nf

@@ -43,6 +43,7 @@ process makeReport {
         path sample_dirs, stageAs: "samples/*"
         path sqanti_dirs, stageAs: "sqanti/*"
         path de_files
+        path "annotation_reference_summary.tsv"
         val wf_version
     output:
         path "wf-transcriptomes-report.html", emit: report
@@ -63,6 +64,7 @@ process makeReport {
         ${de_args} \
         --versions versions \
         --params params.json \
+        --ref_summary annotation_reference_summary.tsv \
         --wf_version ${wf_version}
     """
 }
@@ -202,6 +204,7 @@ workflow pipeline {
             sample_dirs_for_report,
             sqanti_dirs_for_report,
             de_dir,
+            transcriptome.annotation_reference_summary,
             workflow.manifest.version
         )