diff --git a/cpg_utils/hail_batch.py b/cpg_utils/hail_batch.py index ffe4946..6a42e2e 100644 --- a/cpg_utils/hail_batch.py +++ b/cpg_utils/hail_batch.py @@ -295,10 +295,7 @@ def fasta_res_group(b: hb.Batch, indices: list[str] | None = None): @param b: Hail Batch object. @param indices: list of extensions to add to the base fasta file path. """ - ref_fasta = get_config()['workflow'].get('ref_fasta') or reference_path( - 'broad/ref_fasta' - ) - ref_fasta = to_path(ref_fasta) + ref_fasta = reference_path('broad/ref_fasta') d = dict( base=str(ref_fasta), fai=str(ref_fasta) + '.fai',