Merge pull request #367 from kedhammar/aviti-umis

For AVITI manifests, if idx2 cycles > 12 and idx2 can't be parsed, treat it as UMI

VERSIONLOG.md

@@ -1,5 +1,9 @@
 # Scilifelab_epps Version Log
 
+## 20240930.1
+
+For AVITI manifest generation, assume idx2 > 12 cycles and no idx2 parsed means idx2 is UMI and add Ns to manifest.
+
 ## 20240925.1
 
 Add 10X steps to comments-to-running-notes config.

scripts/generate_aviti_run_manifest.py

@@ -189,7 +189,11 @@ def get_manifests(process: Process, manifest_root_name: str) -> list[tuple[str,
                     row["Index1"], row["Index2"] = idx
                 else:
                     row["Index1"] = idx
-                    row["Index2"] = ""
+                    # Assume long idx2 from recipe + no idx2 from label means idx2 is UMI
+                    if int(process.udf.get("Index read 2", 0)) > 12:
+                        row["Index2"] = "N" * int(process.udf["Index read 2"])
+                    else:
+                        row["Index2"] = ""
                 row["Lane"] = lane
                 row["Project"] = project
                 row["Recipe"] = seq_setup
@@ -231,7 +235,7 @@ def get_manifests(process: Process, manifest_root_name: str) -> list[tuple[str,
         check_distances(rows_to_check)
 
     manifests = []
-    for manifest_type in ["untrimmed", "trimmed", "partitioned"]:
+    for manifest_type in ["untrimmed", "trimmed", "empty", "partitioned"]:
         manifests += make_manifests_by_type(
             df_samples_and_controls, process, manifest_root_name, manifest_type
         )
@@ -307,6 +311,22 @@ def make_manifests_by_type(
         )
         manifests.append((file_name, manifest_contents))
 
+    elif manifest_type == "empty":
+        file_name = f"{manifest_root_name}_empty.csv"
+
+        runValues_section = "\n".join(
+            [
+                "[RUNVALUES]",
+                "KeyName, Value",
+                f'lims_step_name, "{process.type.name}"',
+                f'lims_step_id, "{process.id}"',
+                f'manifest_file, "{file_name}"',
+            ]
+        )
+
+        manifest_contents = "\n\n".join([runValues_section, settings_section])
+        manifests.append((file_name, manifest_contents))
+
     elif manifest_type == "partitioned":
         # Drop PhiX controls, to be re-added by length
         df = df[df["Project"] != "Control"]