Finalise 0.7 release

README.md

@@ -1,6 +1,6 @@
 # Anglerfish
 
-[![Anglerfish CI Status](https://github.com/remiolsen/anglerfish/workflows/Anglerfish/badge.svg)](https://github.com/remiolsen/anglerfish/actions)
+[![Anglerfish CI Status](https://github.com/NationalGenomicsInfrastructure/anglerfish/workflows/Anglerfish/badge.svg)](https://github.com/NationalGenomicsInfrastructure/anglerfish/actions)
 [![PyPI](https://img.shields.io/pypi/v/bio-anglerfish)](https://pypi.python.org/pypi/bio-anglerfish/)
 [![Conda (channel only)](https://img.shields.io/conda/vn/bioconda/anglerfish)](https://anaconda.org/bioconda/anglerfish)
 [![Docker Container available](https://img.shields.io/docker/automated/remiolsen/anglerfish.svg)](https://hub.docker.com/r/remiolsen/anglerfish/)
@@ -30,7 +30,7 @@ conda install -c bioconda anglerfish
 ### Install development version
 
 ```
-pip install --upgrade --force-reinstall git+https://github.com/remiolsen/anglerfish.git
+pip install --upgrade --force-reinstall git+https://github.com/NationalGenomicsInfrastructure/anglerfish.git
 ```
 
 ### For Arm64 processors (e.g. Apple M2)
@@ -53,7 +53,7 @@ Additionaly, if Docker is your cup of tea, the Dockerfile supplied in this repos
 For x86 processors (e.g. Intel/AMD):
 
 ```
-git clone https://github.com/remiolsen/anglerfish.git
+git clone https://github.com/NationalGenomicsInfrastructure/anglerfish.git
 cd anglerfish
 # Create a the anglerfish conda environment
 conda env create -f environment.yml
@@ -65,7 +65,7 @@ pip install -e ".[dev]"
 For Arm64 processors (e.g. Apple M1/M2). First [compile and install minimap2 manually](https://github.com/lh3/minimap2?tab=readme-ov-file#installation), then:
 
 ```
-git clone https://github.com/remiolsen/anglerfish.git
+git clone https://github.com/NationalGenomicsInfrastructure/anglerfish.git
 cd anglerfish
 # Create a the anglerfish conda environment (but remove minimap2)
 conda env create -f <(grep -v minimap2 environment.yml)

anglerfish/anglerfish.py

@@ -282,7 +282,7 @@ def run_demux(args):
             closest_sample = min(sample_dists, key=lambda x: x[0])
             # If the distance is more than half the index length, we remove it
             if closest_sample[0] >= (len(i[0]) / 2) + 1:
-                closest_sample = (closest_sample[0], None)
+                top_unknowns.append([i[0], i[1], None])
             else:
                 # We might have two samples with the same distance
                 all_min = [
@@ -297,7 +297,9 @@ def run_demux(args):
                 if all_min:
                     closest_sample = (closest_sample[0], ";".join(all_min))
 
-            top_unknowns.append([i[0], i[1], closest_sample[1]])
+                top_unknowns.append(
+                    [i[0], i[1], f"{closest_sample[1]} ({closest_sample[0]})"]
+                )
         report.add_unmatched_stat(top_unknowns, ont_barcode, adaptor_name)
 
     # Check if there were samples in the samplesheet without adaptor alignments and add them to report

anglerfish/demux/adaptor.py

@@ -1,4 +1,4 @@
-import importlib
+import importlib.resources as resources
 import os
 import re
 
@@ -247,7 +247,7 @@ def load_adaptors(raw: bool = False) -> list[Adaptor] | dict:
     """
 
     # Load adaptors from config file
-    adaptors_config_path = importlib.resources.files("anglerfish.config").joinpath(
+    adaptors_config_path = resources.files("anglerfish.config").joinpath(
         "adaptors.yaml"
     )
     assert isinstance(adaptors_config_path, os.PathLike)

setup.py

@@ -18,7 +18,7 @@
 this_directory = Path(__file__).parent
 long_description = (this_directory / "README.md").read_text()
 
-version = "0.7.0dev0"
+version = "0.7.0"
 
 setup(
     name="bio-anglerfish",
@@ -28,7 +28,7 @@
     long_description_content_type="text/markdown",
     author="Remi-Andre Olsen",
     author_email="[email protected]",
-    url="https://github.com/remiolsen/anglerfish",
+    url="https://github.com/NationalGenomicsInfrastructure/anglerfish",
     license="MIT",
     python_requires=">=3.12",
     packages=find_packages(),