Update gnomAD v3 hg38 bed file reference (#54)

reference_generating_scripts/convert_bed_to_interval_list.py

@@ -32,7 +32,7 @@ def get_ref_files(bed_ref: str, sd_ref: str, outfile_path: str) -> None:
 
 
 @click.command()
-@click.option('--bed-ref', required=True, help='String identifier for the BED file from the references.', default='hg38_telomeres_and_centromeres')
+@click.option('--bed-ref', required=True, help='String identifier for the BED file from the references.', default='gnomad/tel_and_cent_bed')
 @click.option('--sd-ref', required=True, help='String identifier for the sequence dictionary file from the references.', default='broad/genome_calling_interval_lists')
 @click.option('--out-ref', required=True, help='Reference path to save the output .interval_list file.', default='hg38_telomeres_and_centromeres_intervals/interval_list')
 def main(bed_ref, sd_ref, out_ref):

references.py

@@ -209,6 +209,7 @@ def is_folder(self) -> bool:
         transfer_cmd=gcs_cp_r,
         files=dict(
             tel_and_cent_ht='telomeres_and_centromeres/hg38.telomeresAndMergedCentromeres.ht',
+            tel_and_cent_bed='telomeres_and_centromeres/hg38.telomeresAndMergedCentromeres.bed',
             lcr_intervals_ht='lcr_intervals/LCRFromHengHg38.ht',
             seg_dup_intervals_ht='seg_dup_intervals/GRCh38_segdups.ht',
             clinvar_ht='clinvar/clinvar_20190923.ht',
@@ -403,13 +404,6 @@ def is_folder(self) -> bool:
             remm_index='ReMM.v0.3.1.post1.hg38.tsv.gz.tbi',
         ),
     ),
-    Source(
-        'hg38_telomeres_and_centromeres',
-        # gnomAD v3 hg38 coordinates for telomeres and centromeres
-        src='gs://gcp-public-data--gnomad/resources/grch38/telomeres_and_centromeres/hg38.telomeresAndMergedCentromeres.bed',
-        dst='hg38/v0/hg38.telomeresAndMergedCentromeres.bed',
-        transfer_cmd=gcs_cp_r,
-    ),
     Source(
         'hg38_telomeres_and_centromeres_intervals',
         # gnomAD v3 hg38 coordinates for telomeres and centromeres converted to interval_list