Code

Release 2.1.0#123

Code

Merged

GallVp merged 53 commits intomainPlant-Food-Research-Open/assemblyqc:mainfrom devPlant-Food-Research-Open/assemblyqc:devCopy head branch name to clipboardAug 2, 2024

+9,208-1,782

Commits

Commits on Jul 17, 2024

• Added a failing test with a no LTR assembly

  GallVp

  committed
  931c560

Commits on Jul 18, 2024

• Now LTR Retriever does not crash

  GallVp

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  1ae1d5e

• Version bumped and added changelog

  GallVp

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  0974e6a

• cds_length_distribution bug

  GallVp

  committed
  891d9d2

• Merge pull request #96 from Plant-Food-Research-Open/fix/gt

  Show description for 6a30a98
  GallVp

  authored
  6a30a98

• Changed default branch name from master to main

  GallVp

  committed
  d131ba7

Commits on Jul 19, 2024

• Added min. system requirements

  GallVp

  committed
  afba695

• Created summary presence/absence tables for NCBI FCS modules

  GallVp

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  36e5612

• Merge pull request #97 from Plant-Food-Research-Open/fix/master

  Show description for c3ae15a
  GallVp

  authored
  c3ae15a

• Merge pull request #99 from Plant-Food-Research-Open/update/requirements

  Show description for c5e9b56
  GallVp

  authored
  c5e9b56

• Merge branch 'dev' into feature/fcssummary

  GallVp

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  ae6512c

• Fixed linting

  GallVp

  committed
  c9e791d

• Merge pull request #100 from Plant-Food-Research-Open/feature/fcssummary

  Show description for c9620a3
  GallVp

  authored
  c9620a3

• Updated NCBI FCS GX to 0.5.4

  GallVp

  committed
  ca0195b

• Merge pull request #101 from Plant-Food-Research-Open/update/fcsgx

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  GallVp

  authored
  cf49135

• Fixed PLOTSR tokenize bug

  GallVp

  committed
  2abbba5

• Merge pull request #103 from Plant-Food-Research-Open/fix/plotsr

  Show description for 2cdeda3
  GallVp

  authored
  2cdeda3

Commits on Jul 21, 2024

• Updated modules

  GallVp

  committed
  bd23989

• Merge pull request #105 from Plant-Food-Research-Open/update/components

  Show description for b6c428e
  GallVp

  authored
  b6c428e

Commits on Jul 22, 2024

• Allowed LTRRETRIEVER_LTRRETRIEVER to work with read-only assemblies

  GallVp

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  46ce8dd

• Merged dev

  GallVp

  committed
  aa9b7cb

• Merge pull request #106 from Plant-Food-Research-Open/fix/lai

  Show description for a0e4fad
  GallVp

  authored
  a0e4fad

• Updated SYRI to 1.7.0

  GallVp

  committed
  cd571e6

• Merge pull request #107 from Plant-Food-Research-Open/update/syri

  Show description for 336d731
  GallVp

  authored
  336d731

• Moved additional template scripts

  GallVp

  committed
  cf8ba8a

Commits on Jul 23, 2024

• Added script for update checks

  GallVp

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  18e58df

• Updated change log

  GallVp

  committed
  3323335

• Merge pull request #110 from Plant-Food-Research-Open/cleanup

  Show description for 91cc94e
  GallVp

  authored
  91cc94e

• Updated fasta_ltrretriever_lai

  GallVp

  committed
  a1bf0e0

• Merge pull request #111 from Plant-Food-Research-Open/update/ltrretriever_lai

  Show description for ec611cf
  GallVp

  authored
  ec611cf

Commits on Jul 24, 2024

• Updated check_module_versions script

  GallVp

  committed
  26564b7

• Merge pull request #115 from Plant-Food-Research-Open/update/check_module_versions

  Show description for 48e5f5a
  GallVp

  authored
  48e5f5a

Commits on Jul 29, 2024

• Now soft masked regions are unmasked before computing LAI

  GallVp

  committed
  b41d4a0

• Reinstalled fasta_ltrretriever_lai

  GallVp

  committed
  0bee772

• Merge pull request #118 from Plant-Food-Research-Open/unmask/lai

  Show description for 4268dea
  GallVp

  authored
  4268dea

• Updated fastqc and minimap2/align

  GallVp

  committed
  edb9de1

• Removed dependency on PlantandFoodResearch/nxf-modules

  GallVp

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  f6ae2d5

• Updated linting policy

  GallVp

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  733145b

• Updated lint GHA

  GallVp

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  70045af

• Added fastq_fastqc_umitools_fastp

  GallVp

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  a0daa50

• Fixed path

  GallVp

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  c5d285e

• Merge pull request #119 from Plant-Food-Research-Open/updates

  Show description for 41e6331
  GallVp

  authored
  41e6331

Commits on Jul 30, 2024

• Updated citation and fixed typos

  GallVp

  committed
  2a5d0ae

• Updated citation

  GallVp

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  0f1096e

• Updated credits

  GallVp

  committed
  ea2d1c9

• Merge pull request #120 from Plant-Food-Research-Open/typo

  Show description for c5165fe
  GallVp

  authored
  c5165fe

Commits on Jul 31, 2024

• Added a README to the tests directory

  GallVp

  committed
  3cc5ca5

• Added echo for debug on mmc

  GallVp

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  d3b6b07

• Now using the first result from find to link FAlite

  GallVp

  committed
  c697d3b

• Fixed multiple bin binds failure in ASSEMBLATHON_STATS

  GallVp

  committed
  4e86875

• Merge pull request #121 from Plant-Food-Research-Open/debug/mmc

  Show description for de3e6dc
  GallVp

  authored
  de3e6dc

• Merge branch 'dev' into rc/2.1.0

  GallVp

  committed
  2243767

Commits on Aug 2, 2024

• Merge pull request #122 from Plant-Food-Research-Open/rc/2.1.0

  Show description for 8b437a8
  GallVp

  authored
  8b437a8