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Add raw data table output #91

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merged 4 commits into from
Mar 29, 2021
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RaverJay
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@RaverJay RaverJay commented Mar 26, 2021

  • implements Summary report also in text table format #88
  • always adds a .csv and a .xlsx data table to the poreCov output
  • columns:
    sample | kraken2_numreads_sarscov2 | kraken2_numreads_human | kraken2_numreads_unclassified | kraken2_numreads_total | president_identity | president_mismatches | president_percentN | president_numN | president_QC_pass | pangolin_lineage | pangolin_probability | nextclade_clade | nextclade_mutations | nextclade_deletions
  • sample:
    poreCov_summary_report_2021-03-26--16-25-44_datatable.xlsx
  • new fastcov container (added openpyxl package)

@hoelzer
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hoelzer commented Mar 26, 2021

@RaverJay awesome! really helpful.

I can approve this PR.

Just a minor suggestion: what do you guys think about a TSV instead of a CSV? E.g. the nextclade_mutations column has also , and if I e.g. parse the current csv w/ e.g. awk I will run into problems. A proper \tab separation might be safer because we don't run into issues with , being part of any output strings.

@replikation
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@hoelzer @RaverJay yep tab separated is better/saver than csv

@replikation replikation linked an issue Mar 29, 2021 that may be closed by this pull request
@replikation replikation added the enhancement New feature or request label Mar 29, 2021
@RaverJay RaverJay self-assigned this Mar 29, 2021
@replikation replikation merged commit edf65d5 into replikation:master Mar 29, 2021
@replikation
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@RaverJay added tsv to your script.

@RaverJay RaverJay deleted the add_table_output branch March 30, 2021 12:49
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Summary report also in text table format
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