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Add agat sp add start and stop#122

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Leila011 wants to merge 19 commits intomainviash-hub/biobox:mainfrom add-agat_sp_add_start_and_stopviash-hub/biobox:add-agat_sp_add_start_and_stopCopy head branch name to clipboard

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Commits on Aug 6, 2024

• add help

  Leila011

  committed
  2ca5f31

• add config

  Leila011

  committed
  e2b4579

• add run script

  Leila011

  committed
  91aff76

• add test data & expected output + script to fetch them

  Leila011

  committed
  9516e0a

• add test

  Leila011

  committed
  31e30f7

• run script: add unset flag rule for extend

  Leila011

  committed
  cf4af14

• fix test: add --ni flag

  Leila011

  committed
  b3a45ee

• add second test: use --extend flag

  Leila011

  committed
  1e815eb

• update changelog

  Leila011

  committed
  2075456

• config: use --codon as the main argument name instead of --ct

  Leila011

  committed
  bd6fd08

Commits on Aug 7, 2024

• run script: fix verbose usage

  Leila011

  committed
  9669067

Commits on Aug 13, 2024

• Merge main into add-agat_sp_add_start_and_stop

  rcannood

  committed
  94b2848

Commits on Aug 19, 2024

• Merge branch 'main' into add-agat_sp_add_start_and_stop

  Leila011

  authored
  a64927b

• add set -eo pipefail to script and test files

  Leila011

  committed
  19af770

• create temporary directory and clean up on exit

  Leila011

  committed
  33fb44e

• update config: add requirements, add keywords, update --config description

  Leila011

  committed
  083f0c1

Commits on Nov 8, 2024

• Apply suggestions from code review

  Show description for 2d23ac7
  

  rcannood

  and

  dorien-er

  authored
  2d23ac7

• reduce test file size

  rcannood

  committed
  0a1823e

• small fixes

  rcannood

  committed
  6ee2132