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fasta_res_group only points to unmasked reference #125

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fasta_res_group only points to unmasked reference #125

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5 changes: 1 addition & 4 deletions cpg_utils/hail_batch.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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',
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