diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index c7da6a58..42882002 100644 --- a/.github/workflows/main.yml +++ b/.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 diff --git a/workflow/scripts/collect-lineage-variants.py b/workflow/scripts/collect-lineage-variants.py index cf7aa5c4..a811e345 100644 --- a/workflow/scripts/collect-lineage-variants.py +++ b/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])