Development

[jethror1]

• added optional 'report' sheet with ACMG reporting criteria (controlled via --acmg argument)
• remove raising assertion errors when invalid column names specified for --reorder, --rename and --exclude methods
  • a warning is printed and invalid columns removed before continuing, this is to handle where columns may not be present due to panel filtering resulting in a small subset of variants that may not have all fields specified in workflow
• handle empty vcfs passed in, as well as empty vcfs from filtering in app
• minor formatting changes to column widths for SpliceAI

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This change is 

[pep8speaks]

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/excel.py:

Line 235:5: E303 too many blank lines (2) Line 256:80: E501 line too long (85 > 79 characters) Line 257:80: E501 line too long (97 > 79 characters) Line 263:80: E501 line too long (83 > 79 characters) Line 265:80: E501 line too long (80 > 79 characters) Line 267:80: E501 line too long (82 > 79 characters) Line 268:80: E501 line too long (84 > 79 characters) Line 340:9: E303 too many blank lines (2) Line 343:80: E501 line too long (83 > 79 characters)

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

Line 614:80: E501 line too long (82 > 79 characters)

Comment last updated at 2022-04-14 13:37:38 UTC