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tsv cleanup script and workflow#82

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eharkins wants to merge 23 commits intomasternextstrain/ncov-ingest:masterfrom clean-metadatanextstrain/ncov-ingest:clean-metadataCopy head branch name to clipboard

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Commits on Nov 2, 2020

• general tsv cleaner

  

  eharkins

  authored and

  kairstenfay

  committed
  bd0f961

• add --sort-col to bin/clean-tsv-metadata

  

  eharkins

  authored and

  kairstenfay

  committed
  d7ffc97

• add clean-tsv workflow

  

  eharkins

  authored and

  kairstenfay

  committed
  8b76a51

• clean-tsv-metadata: 0-based sort col + error handle

  

  eharkins

  authored and

  kairstenfay

  committed
  5959b73

• clean-tsv-metadata: fix pandas quotes

  

  eharkins

  authored and

  kairstenfay

  committed
  541c155

• clean-tsv-metadata: correct header arg to_csv

  

  eharkins

  authored and

  kairstenfay

  committed
  bbe727a

• clean-tsv-metadata: allow header and n_cols

  

  eharkins

  authored and

  kairstenfay

  committed
  8f5d995

• clean-tsv-metadata: input file positional arg

  

  eharkins

  authored and

  kairstenfay

  committed
  4ef3b29

• clean-tsv-metadata: rename

  

  eharkins

  authored and

  kairstenfay

  committed
  3c28524

• clean-tsv-metadata: --header -> --no-header

  

  eharkins

  authored and

  kairstenfay

  committed
  a932f6c

• clean-tsv-metadata: add output_file;

  Show description for a7ad918
  

  eharkins

  authored and

  kairstenfay

  committed
  a7ad918

• clean-tsv-metadata: fix column truncation

  

  eharkins

  authored and

  kairstenfay

  committed
  3b8d794

• clean-tsv-metadata: too many col error msg

  

  eharkins

  authored and

  kairstenfay

  committed
  10d3b6f

• clean-tsv: Stop reading in TSV twice

  Show description for 54268fb
  kairstenfay

  committed
  54268fb

• clean-tsv: Guard against negative and 0 --n-cols

  Show description for 83bc065
  kairstenfay

  committed
  83bc065

• clean-tsv: Improve --sort-col error message

  Show description for 920a598
  kairstenfay

  committed
  920a598

• clean-tsv: Add type hints to functions

  kairstenfay

  committed
  6d9ec07

• clean-tsv: Fix typo

  kairstenfay

  committed
  fb99922

• clean-tsv: Wrap long lines

  Show description for 40a62a0
  kairstenfay

  committed
  40a62a0

• clean-tsv: Print TSV to stdout by default

  Show description for 37b8814
  kairstenfay

  committed
  37b8814

• clean-tsv: Add --sort option

  Show description for b7edc34
  kairstenfay

  committed
  b7edc34

• Add a script for cleaning manually maintained TSVs

  Show description for 01ee180
  

  kairstenfay

  and

  eharkins

  committed
  01ee180

• Revert "add clean-tsv workflow"

  Show description for 22cef3f
  kairstenfay

  committed
  22cef3f