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fix: gnomAD constraints build
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holtgrewe committed Sep 6, 2024
1 parent 5627632 commit 4fd607c
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Showing 2 changed files with 2 additions and 1 deletion.
2 changes: 1 addition & 1 deletion environment.yml
Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,7 @@ dependencies:
- annonars =0.39.0
- viguno =0.3.1
- mehari =0.25.5
- varfish-server-worker =0.12.0
- varfish-server-worker =0.13.0
# S3 uploads
- s5cmd =2.1.0
# async HTTP requests
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1 change: 1 addition & 0 deletions rules/work/genes/gnomad.smk
Original file line number Diff line number Diff line change
Expand Up @@ -149,6 +149,7 @@ def run_genes_gnomad_constraints_v4_to_tsv(input, output, wildcards):
head -n 1 {input.tsv} \
> $TMPDIR/tmp.tsv
tail -n +2 {input.tsv} \
| grep ENSG \
| sort -k3,3r \
| sort -k1,1 -u \
| sed -e 's/","/"__COMMA__"/g' \
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