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

Job showing workbook follows current format provided by uranus pipeline -> https://platform.dnanexus.com/panx/projects/Gjk2JvQ4z5v8fJJ72f5Bxy3Z/monitor/job/Gv94G004z5vBb3QPXp61ZxQQ

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 588:5: E303 too many blank lines (2)
Line 628:5: E303 too many blank lines (2)
Line 687:5: E303 too many blank lines (2)
Line 746:5: E303 too many blank lines (2)
Line 819:5: E303 too many blank lines (2)
Line 921:5: E303 too many blank lines (2)
Line 977:5: E303 too many blank lines (2)
Line 1002:5: E303 too many blank lines (2)
Line 1026:5: E303 too many blank lines (2)

Comment last updated at 2024-10-18 11:19:16 UTC

[jethror1]

Checking commits to the IN-500-eggd-generate-variant-workbook-v-2-9-0 branch to show previous reviews and merges:

$ git log --first-parent --oneline --pretty=format:'%h %ad %<(20)%an %s' --expand-tabs --abbrev-commit --date=short master..
f74a398 2024-10-18 Jethro Rainford      Merge pull request #200 from eastgenomics/IN-500-make-additional-sheet-consistent-with-main-vcf
37e64dd 2024-10-17 Jethro Rainford      Merge pull request #199 from eastgenomics/IN-500-update-report-text
c29647a 2024-08-30 cnascim1             Merge pull request #197 from eastgenomics/IN-500-space-syntax
a2bc281 2024-05-02 AishaD               rm split test vcf
34e163c 2024-05-01 AishaD               include v2.8.1 and v2.8.2
05dbcf9 2024-05-01 AishaD               merge conflicts
a95187d 2024-04-26 Jay-Miles            Merge pull request #195 from eastgenomics/IN-500-syntax-fix
e571c37 2024-04-25 Jethro Rainford      Merge pull request #194 from eastgenomics/URA-679-bug-fix-additional-files-doesnt-include-exclude
2386f31 2024-04-24 Jethro Rainford      Merge pull request #193 from eastgenomics/IN-500-samplecolumn-duplicated
8a9804f 2024-04-23 Jethro Rainford      Merge pull request #192 from eastgenomics/IN-510-unit-test-new-features
f663294 2024-04-17 Jay-Miles            Merge pull request #191 from eastgenomics/IN-534-bug-fix-pecan-link-needs-updating
5d62e3a 2024-03-21 Aisha                Merge pull request #185 from eastgenomics/IN-511-handle_vcfs_in_additional_files
bd0f3c3 2024-03-20 Jethro Rainford      Merge pull request #184 from eastgenomics/IN-500-update-version
817bdb0 2024-03-20 Jethro Rainford      Merge pull request #183 from eastgenomics/IN-503-option-to-have-af-presented-as-a-decimal-or-percentage
b783b6f 2024-03-20 Jethro Rainford      Merge pull request #181 from eastgenomics/IN-502-make-a-uranus-summary-sheet
5de5ad4 2024-03-20 Jethro Rainford      Merge pull request #179 from eastgenomics/IN-501-add-a-report-text

[jethror1]

Reviewed 6 of 9 files at r1, 3 of 3 files at r2, all commit messages.
Reviewable status: complete! all files reviewed, all discussions resolved (waiting on @Aisha-D)