Code

Wrap up v3.3.3#121

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Merged

fmalmeida merged 55 commits intomasterfmalmeida/bacannot:masterfrom devfmalmeida/bacannot:devCopy head branch name to clipboardMar 11, 2024

+351-424

Commits

Commits on Feb 8, 2023

• Add pre-formatted database (#82)

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  fmalmeida

  authored
  c5fdfbd

Commits on Feb 28, 2023

• 50 add tool integron finder 20 (#87)

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  fmalmeida

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  548147a

Commits on Mar 3, 2023

• 85 prokka module can get after modules stuck if the header file longer than 20 and not separated by tab or space (#89)

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  fmalmeida

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  6fff59a

• fix bakta stats parsing

  fmalmeida

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  36195ff

Commits on Mar 26, 2023

• 81 add tool mob suite (#90)

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  fmalmeida

  authored
  c178c92

Commits on May 4, 2023

• update singularity config

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  567b2bd

Commits on May 5, 2023

• fixed kofamscan download

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  dedef45

Commits on May 6, 2023

• fix dockerfile

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  c2556ee

• Fix unicycler tag

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  a934e4b

• Merge branch 'dev' of https://github.com/fmalmeida/bacannot into dev

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  8f0d9a5

Commits on May 7, 2023

• use only docker images to avoid timeout error

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  460ceac

• use docker ocntainer to avoid singularity timeout

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  f527af2

• fixed resfinder for singularity

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  62e63c5

• fixed docker image

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  67f9942

Commits on May 8, 2023

• fix gff2sql in singularity

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  a726274

Commits on May 9, 2023

• use proper singularity images

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  a9fa23e

• fix singularity image download

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  c470d56

• fixed docker image

  fmalmeida

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  b0ab903

Commits on May 18, 2023

• Add option for prebuilt db download (#94)

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  fmalmeida

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  4c33abf

Commits on May 19, 2023

• 69 tools to use own docker image (#91)

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  fmalmeida

  authored
  5c126dc

Commits on Jul 20, 2023

• update unicycler version (0.5.0--py310h6cc9453_3)

  fmalmeida

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  dd9c4f2

Commits on Jul 26, 2023

• 96 error summary for bugfix release (#101)

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  fmalmeida

  authored
  1ed4a8e

Commits on Sep 18, 2023

• 98 include ices and prophage annotation in json summary (#106)

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  fmalmeida

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  9dc44c5

Commits on Sep 25, 2023

• 100 update pipeline docker images from docker tags to docker shasum (#108)

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  fmalmeida

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  78d0f4f

Commits on Sep 26, 2023

• 107 duplicate reads to unique read names (#109)

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  fmalmeida

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  e36f991

• update changelog

  fmalmeida

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  04bb226

Commits on Oct 1, 2023

• Update docs for v3.3 (#110)

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  fmalmeida

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  520fd3f

• update citation information

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  committed
  93a62ee

• add citation example

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  ae51e18

• Merge branch 'master' of https://github.com/fmalmeida/bacannot into dev

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  5db913d

• Update CHANGELOG.md

  fmalmeida

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  1c28330

Commits on Oct 29, 2023

• 111 error on summary step when missing annotationidtxt key (#112)

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  fmalmeida

  authored
  529d414

• Merge branch 'master' of https://github.com/fmalmeida/bacannot into dev

  fmalmeida

  committed
  880e871

Commits on Feb 20, 2024

• Merge branch 'master' of https://github.com/fmalmeida/bacannot into dev

  fmalmeida

  committed
  ce413c6

• update version

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  6975eac

• add new params

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  fmalmeida

  committed
  15f94a2

Commits on Feb 22, 2024

• add documentation on new parameters

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  2670dd9

• fix typo

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  89c5cbe

• Merge pull request #119 from fmalmeida/118-add-skip-integron-finder-param

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  fmalmeida

  authored
  d04cd83

Commits on Mar 6, 2024

• fix code so that it also runs for singularity

  fmalmeida

  committed
  d0741d6

Commits on Mar 7, 2024

• fixed installation problem for singularity

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  3fbfc91

Commits on Mar 8, 2024

• split antismash docker image and modify module to have custom snippet for singularity in order to avoid problems related to read-only filesystem that happens with this tool

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• also remove the tar.gz

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  25ad59f

• fix misc image

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  a91d4e8

• update used docker images

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  b756408

• update docker image

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  b9b9b69

• update module

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  a68d260

Commits on Mar 9, 2024

• try again to use auto-tests

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  19dd1fc

• simplify types

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  dd0c344

• update changelog

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  126d37f

• fix cli

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  696ab30

• it fails to publish, lets resume

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  80d34ab

Commits on Mar 11, 2024

• add better information on singularity variables

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  74f5100

• fix paths of where versions are stored

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  0cb1b00

• update changelog with date

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  2ff9e2d