IN-511 handle vcfs as additional files

eastgenomics / eggd_generate_variant_workbook

DNAnexus app for generating xlsx variant workbooks

3 stars 0 forks source link

IN-511 handle vcfs as additional files #185

Closed jethror1 closed 3 months ago

jethror1 commented 3 months ago

Handle VCFs passed to --additional_files (i.e from Pindel) and format them accordingly
- Reuses a lot of the vcf methods for parsing and formatting
- Change some of the vcf methods to return lists of vcfs instead of directly formatting the vcfs attribute to fit with the above
Reformat the creation of Report text field to separate vcf.format_report_text() function to get rid of the mega lambda
Minor formatting changes
Fix borked tests from above changes
Fixes #139

This change is

pep8speaks commented 3 months ago

Hello @jethror1! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

In the file resources/home/dnanexus/generate_workbook/utils/vcf.py:

Line 428:37: E225 missing whitespace around operator Line 573:5: E303 too many blank lines (2) Line 613:5: E303 too many blank lines (2) Line 784:5: E303 too many blank lines (2) Line 953:5: E303 too many blank lines (2) Line 977:5: E303 too many blank lines (2)

eastgenomics / eggd_generate_variant_workbook

IN-511 handle vcfs as additional files #185

Comment last updated at 2024-03-21 14:21:51 UTC