diff --git a/reference_generating_scripts/convert_bed_to_interval_list.py b/reference_generating_scripts/convert_bed_to_interval_list.py index 3a7ad67..a7b285e 100644 --- a/reference_generating_scripts/convert_bed_to_interval_list.py +++ b/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): diff --git a/references.py b/references.py index 3534207..c3e9074 100644 --- a/references.py +++ b/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