fix: update link for covariants (#626)

* update link

* fmt

* Update super linter in main.yml

* Update main.yml

* Update collect-lineage-variants.py

* Update collect-lineage-variants.py

.github/workflows/main.yml

@@ -24,7 +24,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Formatting
-        uses: github/super-linter@v5.0.0
+        uses: super-linter/super-linter@v5.7.2
         env:
           VALIDATE_ALL_CODEBASE: false
           DEFAULT_BRANCH: master

workflow/scripts/collect-lineage-variants.py

@@ -18,7 +18,7 @@
 from requests.models import ContentDecodingError
 
 covariants_data = requests.get(
-    "https://raw.githubusercontent.com/hodcroftlab/covariants/master/web/data/clusters.json"
+    "https://raw.githubusercontent.com/hodcroftlab/covariants/master/web/public/data/clusters.json"
 ).json()
 translate_aa = get_backtranslation_table("Standard")
 gff = gffutils.create_db(snakemake.input.annotation, dbfn=":memory:")
@@ -327,5 +327,4 @@ def write_record(pos, ref_allele, alt_allele, lineages, variants):
 
             ref_allele = infasta.fetch(reference=contig, start=pos, end=pos + 3)
             for alt_allele in aa_to_dna(variant.right):
-
                 write_record(pos, ref_allele, alt_allele, lineages, [variant])