COVID-19: variation analysis reporting

This workflow takes VCF datasets of variants produced by any of the "*-variant-calling" workflows in https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling and generates tabular reports of variants by samples and by variant, along with an overview plot of variants and their allele-frequencies across all samples.

Changelog

[0.3.4] 2024-09-24

Automatic update

• toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0 was updated to toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy0 was updated to toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy0 was updated to toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1
• toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.1 was updated to toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy0 was updated to toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1

[0.3.2] 2023-11-28

Automatic update

• toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2 was updated to toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0
• toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0 was updated to toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.1

[0.3.1] 2023-11-20

• Fix author in dockstore

[0.3] 2022-10-13

Changed

• Upgraded to new, more flexible version of column_maker tool.

  This change allows a simplification of the workflow, which now uses two steps less for producing identical results.

• Upgraded to latest version of tp_find_and_replace tool, which can handle multiple substitutions per tool run. Saves another step in the workflow.

• Upgraded datamash to its latest tool wrapper version.

These changes should not have any effects on results except this one:

• the AFcaller column of the "Combined Variant Report by Sample" could previously contain values in scientific notation for very low allele frequencies (< 0.001). In the new version all values in the column will be reported consistently in regular floating point format.

[0.2] 2022-02-11

Changed

• Altered the exact meaning of the user-supplied AF and DP_ALT thresholds

  The AF threshold is now compared against (DP4[2] + DP4[3]) / DP, i.e. the unbiased AF based on all bases at the site instead of against the AF reported by the variant caller (which in the case of lofreq would consider only variant-supporting bases >= the caller's --min-bq in the numerator).

  Conversely, the DP_ALT threshold is now compared against DP * AF (as reported by the variant caller), i.e. in the case of lofreq as the caller will consider only bases with >= --min-bq base quality.

• Reported AF values in the by-sample and the by-variant reports are now unbiased AF values calculated from (DP4[2] + DP4[3]) / DP as explained above.

  The by-sample report reports the original AF value provided by the variant caller in an additional AFcaller column.

• Tile colors in the variant frequency summary plot are now based on unbiased AF values.

• An extra step removing potential called variants with a caller-reported DP of 0 has been added to avoid division by zero errors in the calculation of unbiased AF values.

Fixed

• Reverted the autoupdated wrapper version change for the snpsift tools

  The autoupdate script had problems sorting their non-standard version strings correctly and downgraded these wrappers instead of upgrading them

• Made sure only a single changeset revision of the text_processing tools is used in the workflow.

[0.1.3] 2022-02-04

Automatic update

• toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1 was updated to toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3.0
• toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0 was updated to toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3.0
• toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2 was updated to toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
• toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.5 was updated to toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6

[0.1.2] 2021-12-13

Added

• Added GitHub Actions workflow. No functional changes.

[0.1.1] 2021-07-23

Added

Added RO-Crate metadata file. No functional changes.

[0.1]

• Initial version of COVID-19: variation analysis reporting

The following tools are required to run this workflow.

This will eventually be a pretty page with links to each tool in the (new) toolshed, etc.

• toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1
• toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
• toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0
• toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2
• toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1
• toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1
• toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
• Filter1
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1
• Cut1
• toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1
• toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3