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genomic-medicine-sweden / tomte

A nextflow pipeline for analysing expression and splicing in RNA seq data from rare disease patient
MIT License
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Give systematic naming to columns from DROP output #131

Closed Lucpen closed 5 months ago

Lucpen commented 5 months ago

Description of the bug

Column naming is not so systematic (many in camel case, some that useunderscores, some that mix, some with ALL CAPS, some all lower without any separators). Also some unused columns by the looks of it, esp for fraser? Like GENE_COUNTS_FILE, SPLICE_COUNTS_DIR, DNA_ID aso.

Command used and terminal output

No response

Relevant files

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System information

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dnil commented 5 months ago

I have a feeling the ideal would be to pass this one level up to make it match the DROP documentation, but having all in one convention would sure be pretty!

Lucpen commented 5 months ago

The captails separated by _ come form the annotation table, I could make them into camel case and that way everything would match