Minor changes and bug fixes

[jethror1]

• fix bug in not adding sample name to exclude sheet when --add_samplename_column specified
• fix uploading intermediate vcfs from app with -keep_tmp
• updates to readme
• add method to verify no variants dropped after filtering and intersecting
• minor improvements to app code and formatting
• adjust widths and formatting of variant columns in worksheets
• correctly handle adding panel and clinical indication strings to summary sheet for dias
• change to make rename method to use CSQ prefix to be consistent with other methods

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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/generate_workbook.py:

Line 49:5: E303 too many blank lines (2)

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

Line 335:5: E303 too many blank lines (2) Line 352:5: E303 too many blank lines (2)

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

Line 147:5: E303 too many blank lines (2)

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

Line 52:80: E501 line too long (94 > 79 characters) Line 53:80: E501 line too long (87 > 79 characters) Line 106:80: E501 line too long (81 > 79 characters) Line 591:5: E303 too many blank lines (2) Line 609:80: E501 line too long (81 > 79 characters)

Comment last updated at 2022-04-07 23:08:56 UTC