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feat(browser): update hgdp tutorial download links
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@rileyhgrant
rileyhgrant committed May 6, 2024
1 parent 4d7ff61 commit a392b10
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Showing 2 changed files with 388 additions and 47 deletions.
82 changes: 60 additions & 22 deletions browser/src/DownloadsPage/GnomadV3Downloads.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -195,7 +195,7 @@ const GnomadV3Downloads = () => (
<ListItem>
<DownloadLinks
label="Sample metadata TSV"
path="/release/3.1.2/vcf/genomes/gnomad.genomes.v3.1.2.hgdp_1kg_subset_sample_meta.tsv.bgz"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/metadata_and_qc/gnomad_meta_updated.tsv"
/>
</ListItem>
{hgdpAnd1kgChromosomeVcfs.map(({ chrom, size, md5 }) => (
Expand Down Expand Up @@ -435,86 +435,100 @@ const GnomadV3Downloads = () => (
<ListItem>
<DownloadLinks
label="Sample metadata TSV"
path="/release/3.1/secondary_analyses/hgdp_1kg/metadata_and_qc/gnomad_meta_v1.tsv"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/metadata_and_qc/gnomad_meta_v1.tsv"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<GetUrlButtons
label="Subset of the HGDP+1KG callset MatrixTable"
path="/release/3.1/secondary_analyses/hgdp_1kg/pca_preprocessing/ld_pruned.mt"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/pca_preprocessing/ld_pruned.mt"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<GetUrlButtons
label="Related sample IDs Hail Table"
path="/release/3.1/secondary_analyses/hgdp_1kg/pca_preprocessing/related_sample_ids.ht"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/pca_preprocessing/related_sample_ids.ht"
/>
</ListItem>

{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<GetUrlButtons
label="Principal component analysis (PCA) PC score tables GCS Bucket"
path="/release/3.1/secondary_analyses/hgdp_1kg/pca/pc_scores_with_outliers/"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/pca/pc_scores_with_outliers/"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<DownloadLinks
label="PCA outliers table"
path="/release/3.1/secondary_analyses/hgdp_1kg/pca/pca_outliers.txt"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/pca/pca_outliers.txt"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<GetUrlButtons
label="PCA PC score tables without outliers GCS Buckets"
path="/release/3.1/secondary_analyses/hgdp_1kg/pca/pc_scores_without_outliers/"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/pca/pc_scores_without_outliers/"
/>
</ListItem>

{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<GetUrlButtons
label="Variants and unrelated samples MatrixTable"
path="/release/3.1/secondary_analyses/hgdp_1kg/pca_results/unrelateds_without_outliers.mt"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/pca_results/unrelateds_without_outliers.mt"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<GetUrlButtons
label="Variants and related samples MatrixTable"
path="/release/3.1/secondary_analyses/hgdp_1kg/pca_results/relateds_without_outliers.mt"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/pca_results/relateds_without_outliers.mt"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<DownloadLinks
label="Population-level statistical summary TSV"
path="/release/3.1/secondary_analyses/hgdp_1kg/metadata_and_qc/post_qc_summary.tsv"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/metadata_and_qc/post_qc_summary.tsv"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<DownloadLinks
label="Doubleton counts CSV"
path="/release/3.1/secondary_analyses/hgdp_1kg/f2_fst/doubleton_count.csv"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/f2_fst/doubleton_count.csv"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<GetUrlButtons
label="Variants and unrelated sample PLINK files"
path="/release/3.1/secondary_analyses/hgdp_1kg/f2_fst/hgdp_tgp*"
label="Variants and unrelated sample PLINK files - .bed"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/f2_fst/hgdp_tgp.bed"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<GetUrlButtons
label="Variants and unrelated sample PLINK files - .bim"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/f2_fst/hgdp_tgp.bim"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<GetUrlButtons
label="Variants and unrelated sample PLINK files - .fam"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/f2_fst/hgdp_tgp.fam"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<DownloadLinks
label="Population-level mean fixation index table"
path="/release/3.1/secondary_analyses/hgdp_1kg/f2_fst/mean_fst.txt"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/f2_fst/mean_fst.txt"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
Expand Down Expand Up @@ -542,7 +556,7 @@ const GnomadV3Downloads = () => (
<ListItem>
<GetUrlButtons
label="HGDP+1KG and GVV intersection Matrix Table"
path="/release/3.1/secondary_analyses/hgdp_1kg/data_intersection/hgdp_tgp_ggv_intersect.mt"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/data_intersection/hgdp_tgp_ggv_intersect.mt"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
Expand All @@ -565,21 +579,21 @@ const GnomadV3Downloads = () => (
<ListItem>
<GetUrlButtons
label="Pre-QC column fields Hail Table"
path="/release/3.1/secondary_analyses/hgdp_1kg/plot_datasets/pre_qc_plotting.ht"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/plot_datasets/pre_qc_plotting.ht"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<GetUrlButtons
label="Pre-QC expected heterozygosity Hail Table"
path="/release/3.1/secondary_analyses/hgdp_1kg/plot_datasets/expected_hets_pre_qc.ht"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/plot_datasets/expected_hets_pre_qc.ht"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<GetUrlButtons
label="Pre-QC actual heterozygosity Hail Table"
path="/release/3.1/secondary_analyses/hgdp_1kg/plot_datasets/actual_hets_pre_qc.ht"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/plot_datasets/actual_hets_pre_qc.ht"
/>
</ListItem>

Expand All @@ -588,28 +602,52 @@ const GnomadV3Downloads = () => (
<ListItem>
<GetUrlButtons
label="Post-QC column fields Hail Table"
path="/release/3.1/secondary_analyses/hgdp_1kg/plot_datasets/post_qc_plotting.ht"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/plot_datasets/post_qc_plotting.ht"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<GetUrlButtons
label="Post-QC expected heterozygosity Hail Table"
path="/release/3.1/secondary_analyses/hgdp_1kg/plot_datasets/expected_hets_post_qc.ht"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/plot_datasets/expected_hets_post_qc.ht"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<GetUrlButtons
label="Post-QC actual heterozygosity Hail Table"
path="/release/3.1/secondary_analyses/hgdp_1kg/plot_datasets/actual_hets_post_qc.ht"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/plot_datasets/actual_hets_post_qc.ht"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<DownloadLinks
label="Post-QC site frequency spectrum table"
path="/release/3.1/secondary_analyses/hgdp_1kg/plot_datasets/sfs_post_qc.txt"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/plot_datasets/sfs_post_qc.txt"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<DownloadLinks
label="Phased haplotype ChrX PAR1"
path="/resources/hgdp_1kg/phased_haplotypes_v2/hgdp1kgp_chrX_par1.shapeit5_common.bcf"
associatedFileType="CSI"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<DownloadLinks
label="Phased haplotype ChrX PAR2"
path="/resources/hgdp_1kg/phased_haplotypes_v2/hgdp1kgp_chrX_par2.shapeit5_common.bcf"
associatedFileType="CSI"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<DownloadLinks
label="Phased haplotype ChrX Non-PAR"
path="/resources/hgdp_1kg/phased_haplotypes_v2/hgdp1kgp_chrX_non_par.full.shapeit5_rare.bcf"
associatedFileType="CSI"
/>
</ListItem>
</FileList>
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