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eastgenomics / eggd_generate_variant_workbook

DNAnexus app for generating xlsx variant workbooks
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Add version workflow + flagstat reads numbers #6

Closed Yu-jinKim closed 4 years ago

Yu-jinKim commented 4 years ago

This change is Reviewable

Yu-jinKim commented 4 years ago

src/vcf2xls_nirvana.sh, line 82 at r1 (raw file):

Previously, mattgarner wrote…
> ``` > dx download "project-Fjj60Qj4yBGvQXbb5Z6FXkgF:file-Fk0X8704yBGYGJYp09xBqkK0" -o exons_nirvana203 > dx download "project-Fjj60Qj4yBGvQXbb5Z6FXkgF:file-FkPp44j4yBGbVbPz1xFZ59PB" -o BioinformaticManifest > dx download "project-Fjj60Qj4yBGvQXbb5Z6FXkgF:file-Fk0X2Q04yBGZvF276zYpbfK1" -o nirvana_genes2transcripts > ``` Manifest and transcripts are dynamic files, so the ids will change over time. Can we make these inputs rather than hardcoded so we don't have to change this app whenever the files are updated?

Should probably add the genepanels file too. Is the exon_nirvana file going to change with the next versions of nirvana? Or is it not that "dynamic" that we can keep it as hard coded?