Update artic to 1.5.1

recipes/artic/meta.yaml

@@ -1,6 +1,6 @@
 {% set name = "artic" %}
-{% set version = "1.2.4" %}
-{% set sha256 = "981219a49cec01dc82a9375b16f844278e797ad4034efa1eaa410ccb1849c617" %}
+{% set version = "1.5.1" %}
+{% set sha256 = "6bbd5f07f1417ff046bdc17c57cf55871027738e082121e24c5b22593351d27b" %}
 
 package:
   name: {{ name|lower }}
@@ -10,70 +10,61 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 1
+  number: 0
   noarch: python
   run_exports:
     - {{ pin_subpackage('artic', max_pin='x.x') }}
   script: python -m pip install --ignore-installed .
   entry_points:
     - artic=artic.pipeline:main
     - align_trim=artic.align_trim:main
-    - align_trim_n=artic.align_trim_n:main
     - margin_cons=artic.margin_cons:main
-    - margin_cons_medaka=artic.margin_cons_medaka:main
     - vcfextract=artic.vcfextract:main
     - artic_vcf_merge=artic.vcf_merge:main
     - artic_vcf_filter=artic.vcf_filter:main
     - artic_make_depth_mask=artic.make_depth_mask:main
     - artic_fasta_header=artic.fasta_header:main
     - artic_mask=artic.mask:main
-    - artic_get_stats=artic.artic_mqc:main
+    - artic_get_models=artic.get_models:main
 
 requirements:
   host:
-    - python >=3
+    - python ==3.9
     - pip
+    - setuptools
   run:
-    - python
-    - artic-porechop >=0.3.2pre
-    - artic-tools
-    - longshot
+    - python ==3.9
     - bcftools
     - biopython
     - bwa
+    - clair3
     - clint
     - htslib
-    - medaka >=1.10.0
-    - minimap2 >=2.26
+    - minimap2
     - multiqc
-    - muscle =3.8
-    - nanopolish >=0.14.0
+    - muscle <5.1
     - pandas
     - pip
     - pysam
     - pytest 
-    - pyvcf
+    - cyvcf2
     - pyfaidx =0.6.0 # DO NOT CHANGE THIS PIN UNDER ANY CIRCUMSTANCES, IT WILL BREAK THE PIPELINE
     - requests
     - samtools
     - tqdm
-    - keras-preprocessing >=1.1.2
-
 
 test:
   commands:
     - artic -h
     - align_trim -h
-    - align_trim_n -h
     - margin_cons -h
-    - margin_cons_medaka -h
     - vcfextract -h
     - artic_vcf_merge -h
     - artic_vcf_filter -h
     - artic_make_depth_mask -h
     - artic_fasta_header -h
     - artic_mask -h
-    - artic_get_stats -h
+    - artic_get_models -h
 
 about:
     home: https://github.com/artic-network/fieldbioinformatics