Merge remote-tracking branch 'upstream/master' into ont-logbooks

VERSIONLOG.md

@@ -4,6 +4,34 @@
 
 Add logbook for PromethION and MinION.
 
+## 20240910.1
+
+Downprioritize column 3 of PromethION (used by CG), when running script to suggest ports.
+
+## 20240909.1
+
+Fix bug with zika module import cont; Change project format for AVITI run manifest
+
+## 20240902.4
+
+Also include Project name and sequencing setup in AVITI run manifest for PhiX
+
+## 20240902.3
+
+Include Project name and sequencing setup in AVITI run manifest
+
+## 20240902.2
+
+Ruff format
+
+## 20240902.1
+
+Fix bug with zika module import
+
+## 20240901.1
+
+Fix bug with AVITI process
+
 ## 20240830.2
 
 Make ONT volume calculations script case-agnostic for concentration units.

scilifelab_epps/utils/__init__.py

@@ -1,3 +1,6 @@
 """Module for reusable utility functions, within the repo scilifelab/scilifelab_epps.
 Alfred Kedhammar, 2023
 """
+
+from . import formula as formula
+from . import udf_tools as udf_tools

scilifelab_epps/zika/__init__.py

@@ -0,0 +1,2 @@
+from . import methods as methods
+from . import utils as utils

scripts/generate_aviti_run_manifest.py

@@ -122,11 +122,21 @@ def get_samples_section(process: Process) -> str:
                 index1 = label_seq
                 index2 = ""
 
+            # Project name and sequencing setup
+            if sample.project:
+                project = sample.project.name.replace(".", "__").replace(",", "")
+                seq_setup = sample.project.udf.get("Sequencing setup", "0-0")
+            else:
+                project = "Control"
+                seq_setup = "0-0"
+
             row = {}
             row["SampleName"] = sample.name
             row["Index1"] = index1
             row["Index2"] = index2
             row["Lane"] = lane
+            row["Project"] = project
+            row["Recipe"] = seq_setup
 
             lane_rows.append(row)
 
@@ -143,6 +153,8 @@ def get_samples_section(process: Process) -> str:
                 row["Index1"] = phix_idx_pair[0]
                 row["Index2"] = phix_idx_pair[1]
                 row["Lane"] = lane
+                row["Project"] = "PhiX"
+                row["Recipe"] = "0-0"
                 lane_rows.append(row)
 
         # Check for index collision within lane, across samples and PhiX

scripts/manage_demux_stats.py

@@ -998,7 +998,7 @@ def main(process_lims_id, demux_id, log_id):
     fill_process_fields(demux_process, process_stats)
 
     # Create the demux output file
-    if "AVITI" in demux_process.process.type.name:
+    if "AVITI" in demux_process.type.name:
         parser_struct = write_demuxfile_aviti(process_stats, demux_id)
     else:
         parser_struct = write_demuxfile(process_stats, demux_id)

scripts/ont_suggest_ports.py

@@ -42,7 +42,9 @@ def main(lims, args):
 
         # Sort ports (a sort of port sort, if you will)
         ports_list = list(ports.items())
-        ports_list.sort(key=lambda x: x[1])
+        ports_list.sort(
+            key=lambda x: x[1] + 1000 if x[0][0] == "3" else x[1]
+        )  # Sort by port usage, but send column 3 to the end since it's reserved for Clinical Genomics
 
         # Collect which ports are already specified in UDFs
         ports_used = []
@@ -79,7 +81,7 @@ def main(lims, args):
             ports_used.append(port_tuple[0])
 
         # Print ports to stdout, starting with the least used
-        message = f'Listing ports, from least to most used: {", ".join([port[0] for port in ports_list])}'
+        message = f'Listing ports, from least to most used, down-prioritizing column 3: {", ".join([port[0] for port in ports_list])}'
         sys.stdout.write(message)
 
     except AssertionError as e: