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Add RNU-gene and reference files cleanup #231

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merged 3 commits into from
Sep 26, 2024
Merged

Add RNU-gene and reference files cleanup #231

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17d2103
Update reference tools structure and update config to new version
Jakob37 Sep 24, 2024
6d02f51
Logging to distinguish what is new and what is all added from ClinVar…
Jakob37 Sep 26, 2024
5e6597e
Changelog
Jakob37 Sep 26, 2024
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28 changes: 19 additions & 9 deletions .gitignore
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Original file line number Diff line number Diff line change
@@ -1,18 +1,28 @@
# Files
git.hash
nextflow.config
todo
mito_full.nf

# Suffix
*~
__pycache__/
container/*.sif
*.sif
.nextflow*
nextflow.config
work/
*.html
*#
git.hash
todo
mito_full.nf
## ref tools
bin/reference_tools/*.log
bin/reference_tools/*.bed
*.orig
*.tbi

# Folders
__pycache__/
work/
data/
output/
.vscode/

# Ref tools
bin/reference_tools/*.log
bin/reference_tools/*.bed
bin/reference_tools/refdata/*.vcf.gz

3 changes: 3 additions & 0 deletions CHANGELOG.md
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# CHANGELOG

### TBD
* Update config for bed intersect

### 3.9.10
* Use reduced gene_panel JSON to avoid adding dead/archived panels to new scout cases
* Add lennart-side script/worker CRON job to generate new gene panel JSON
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0 ...e_tools/agilient_hg38_nochr_noalt_1-3.bed → ...refdata/agilient_hg38_nochr_noalt_1-3.bed
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1 change: 1 addition & 0 deletions bin/reference_tools/refdata/user_added.bed
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17 43387226 43387417 RNU2-4
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@alkc alkc Sep 25, 2024 •
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Coordinates check out 👍

338 changes: 0 additions & 338 deletions bin/reference_tools/update_bed.pl
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