v2.8.2

Updates:

• Update the lock_sheet function by removing the protection on formatting rows and columns
• Update some titles of tables in the summary page
• Add a new table - ‘MLPA confirmation’ in the summary page

v2.8.0

Updates:

• Add PID box in the summary sheet
• Swap BA1 and BS1 rows in the interpret table
• Increase the number of unlocked row to 500 in all sheets

v2.7.1

Updates:

• Handle VCFs already split with bcftools +split-vep, required for new filtering app that will output VCFs with split VEP annotation
• Fix various unit tests broken in previous PRs and added GitHub action to run unit tests automatically
• Improve RD workbook sheet
  - GEM table was removed in the “summary” sheet
  - “report” sheet was renamed as “interpret”
  - the script was updated so that the number of “interpret” sheet is decided by --acmg args
  - the contents and format of table in “interpret” sheet were updated by
  - adding strength POINTS in col I and L
  - adding POINTS in row 26 col G
  - separating original table into two tables (1st table from row 2 to 6 and 2nd table from row 8 to 26)
  - removing colouring of some cells
  - re-phrasing col B
  - removing PP5 and BP6 rows in the 2nd table
• drop-downs were added in the “interpret” and “included” sheets as below:
  - drop-downs for pathogenic and benign strength columns in “interpret” sheet(s)
  - drop-down items for both pathogenic and benign (except BA1) - “Very Strong, Strong, Moderate, Supporting, NA”
  - drop-down items for BA1 - “Stand-Alone, Very Strong, Strong, Moderate, Supporting, NA”
  - drop-down for ACMG classification in “interpret” sheet(s) with the items - “Pathogenic, Likely Pathogenic, Uncertain Significance, Likely Benign, Benign”
  - drop-downs for each row of variant (if any) in “Interpreted” column in “included/variants” sheet with the items - “YES, NO”
• workbook sheet contents were protected from making changes and workbook sheets are protected from renaming when --lock_sheet is true (in all sheets except “ExcludedRegions” in CNV).

v2.6.0

Summary

Small update to add 'details' metadata to the output .xlsx reports in DNAnexus.

Changes

• Adds DNAnexus details metadata to the output xlsx file, including clinical_indication (if Dias), and variant counts. This is variants if no filtering is performed, included if filtering is performed, plus excluded if variants which do not pass filtering are retained in a separate tab.
• Updates openpyxl version in requirements.txt 3.0.9 → 3.1.2 to match .whl used in app

v2.5.0

Summary

Update to include changes for better parsing of CombinedVariantOutput and MetricsOutput tsv files from Illumina’s TSO500 local app into additional sheets, as well as configurable freezing of column and expanding functionality of hyperlink columns.

Changes

• Parsing of MetricsOutput.tsv

  • When provided to --additional_files, will attempt to parse out column of given sample’s metrics from the file (based off the name of the vcf), and colour the sample values based off the lower and upper guideline values in the file

• Parsing of CombinedVariantOutput.tsv

  • When provided to --additional_files, will parse out the TMB, MSI and Gene Amplifications from the file into an additional sheet

• Additional arg added of --add_classification_column to add an empty column named Classification to the variant sheets for reporting

• Additional arg of --split_hgvs added to split the HGVSc and HGVSp to just the DNA and protein change in separate columns without the transcript

• Additional arg added of --add_raw_change to add a concatenation of CHROM, POS, REF and ALT into a separate column named rawChange

• Restructuring of how additional column hyperlinks are added (i.e. those not coming from VEP annotation) to be more generic, now is parsed from a single argument (--additional_columns) which accepts multiple strings as input (currently: decipher, oncokb, cbioportal and pecan), for which a column will be created with a hyperlink to the respective resources website

• Additional argument of --freeze_column added to handle Excel freezing of a sheet at a given column/row

• Change basic summary sheet to be specific to helios, add in parsing in of specific metrics from MetricsOutput and TMB/MSI/Gene Amplifications values

• Update openpyxl Python package in app from 3.0.9 → 3.1.2

• Additional rounding of column(s) to fixed number of dp to display; currently supports VF column to 2dp

• New inputs:

  • --split_hgvs (bool)

  • --add_raw_change (bool)

  • --add_classification_column (bool)

  • --freeze_column (string)

  • --additional_columns (string; replaces --decipher)

• Obsolete inputs:

  • --decipher (replaced by --additional_columns)

Fixes

#135 Freeze columns up to IMPACT (column O)

v2.4.0

Summary

Small update to improve parsing of reference build from VCF header to display in workbook summary sheet and addition of COSMIC hyperlinks.

Changes

• Improve parsing of reference build from VCF header to display in workbook summary sheet this is now parsed from the assembly field in the ##VEP line of the VCF header to be more robust.
• VEP fields are now parsed to remove duplicates on the same annotation due to multiple transcripts handles known bug in VEP <108.
• COSMIC IDs are now hyperlinked to the website if present in the VCF columns.

v2.3.0

Summary

Update to add conditional colouring of cells in variant sheets

Changes

• add option to colour cells with specified colours based on conditions given via -colour_cells
• addition of basic summary sheet including totals of variants per sheet and DNAnexus IDs etc
• minor formatting changes to Dias summary sheet

v2.2.0

Summary

Update to handle parsing of additional non VCF files and images into additional sheets, and optional column of hyperlinks to variant entries in DECIPHER.

Changes

• Ability to handle parsing in one or more additional files (i.e. tsv, csv bed etc) with --additional_files. Type is inferred through utils.determine_delimeter() and names of sheets may be set through --additional_sheet_names.
• Ability to handle parsing images to additional sheets with --images, valid file types are those given by filetype.is_image(). Sheet names may be set with --image_sheet_names and image sizes may be set with --image_sizes (default is maximum of 1920x1080, retaining original aspect ratio of the image).
• Additional boolean --decipher argument to add optional column of links to entry in DECIPHER for variant sheets by @kjwinfield (n.b. only compatible with build 38 vcfs)

Bug fixes

• Fix setting max column width for additional files - #119

v2.1.1

Summary

Bugfix release to fix issue with typing of numeric values in hyperlinks

Changes

• addition of new utils.is_numeric() to correctly type numeric values in cells
• additional unit test for changes

v2.1.0

Summary

Update to handle generating workbooks for GATK gCNV and llumina TSO500 VCFs annotated with VEP, as well as some minor improvements and bug fixes.

Changes

• Handle GATK cCNV and Illumina TSO500 VCFs
• Freeze header row of variant sheets so it always remains in view on scrolling
• Minor tweaks to column widths for readability

Bug fixes

• Fix missing colouring of BA1 criteria cell in ACMG report template
• Fix broken links in readme