IN-500 eggd_generate_variant_workbook v2.9.0

[Aisha-D]

Changes are mainly to keep uranus-centric features currently provided from the handler app to be presented in the workbook. The changes include:

• Addition of uranus summary page
• Extra "report text" column
• Allow allele frequency to be presented as percent
• Bug fixes;
  • Raise nicer error message on non-VEP annotated VCFs / handle non-VEP VCFs #117
  • PeCan link is apparently broken as the URL has changed :sadpanda: #157
  • Handle VCFs as additional files #139

Testing page: https://cuhbioinformatics.atlassian.net/wiki/spaces/DV/pages/3193929758/eggd+generate+variant+workbook+-+v2.9.0

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This change is 

[pep8speaks]

Hello @Aisha-D! 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/generate_workbook.py:

Line 221:80: E501 line too long (83 > 79 characters)
Line 319:13: E128 continuation line under-indented for visual indent
Line 320:13: E124 closing bracket does not match visual indentation
Line 325:13: E124 closing bracket does not match visual indentation

• In the file resources/home/dnanexus/generate_workbook/tests/test_vcf.py:

Line 212:41: E251 unexpected spaces around keyword / parameter equals
Line 212:43: E251 unexpected spaces around keyword / parameter equals
Line 636:73: E251 unexpected spaces around keyword / parameter equals
Line 636:75: E251 unexpected spaces around keyword / parameter equals
Line 691:1: E302 expected 2 blank lines, found 1
Line 699:80: E501 line too long (89 > 79 characters)
Line 723:80: E501 line too long (89 > 79 characters)
Line 736:27: E222 multiple spaces after operator
Line 743:35: E231 missing whitespace after ','
Line 745:80: E501 line too long (102 > 79 characters)

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

Line 190:5: E303 too many blank lines (2)
Line 191:13: E117 over-indented
Line 224:80: E501 line too long (80 > 79 characters)
Line 264:80: E501 line too long (88 > 79 characters)
Line 289:80: E501 line too long (81 > 79 characters)
Line 1492:26: E203 whitespace before ':'
Line 1846:5: E303 too many blank lines (2)

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

Line 146:80: E501 line too long (84 > 79 characters)

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

Line 428:37: E225 missing whitespace around operator
Line 577:5: E303 too many blank lines (2)
Line 617:5: E303 too many blank lines (2)
Line 676:5: E303 too many blank lines (2)
Line 797:5: E303 too many blank lines (2)
Line 953:5: E303 too many blank lines (2)
Line 966:5: E303 too many blank lines (2)
Line 990:5: E303 too many blank lines (2)

Comment last updated at 2024-08-30 15:35:46 UTC