Code

Merging Feat/selection#23

Code

Merged

GallVp merged 40 commits intomainPlant-Food-Research-Open/genepal:mainfrom feat/selectionPlant-Food-Research-Open/genepal:feat/selectionCopy head branch name to clipboardApr 30, 2024

+8,908-2,782

Commits

Commits on Mar 19, 2024

• Updated project infra, see changelog

  GallVp

  committed
  85b3e2d

Commits on Mar 20, 2024

• Updated modules and subworkflows

  GallVp

  committed
  8d9ee7a

• Now tracking liftoff from nf-core/modules

  GallVp

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  0cea739

Commits on Mar 21, 2024

• Added before

  GallVp

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  f1384ab

• Lightweight stub test and removed file.simpleName bug

  GallVp

  committed
  7ab82cb

Commits on Mar 24, 2024

• Now using 1 round for augustus training for test data

  GallVp

  committed
  458dedf

Commits on Mar 25, 2024

• Now braker can be skipped by providing braker files

  GallVp

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  5dd99c6

• Added gffcompare to merge liftoff annotations

  GallVp

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  4f6feae

• Renamed samplesheet param to fastq

  GallVp

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  fb15149

Commits on Mar 26, 2024

• Now using assemblysheet for inputs

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  9765060

Commits on Mar 27, 2024

• Now using nf-validation to validate fastqsheet provided by params.fastq

  GallVp

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  12a66ea

• Moved manifest.config and reporting_defaults.config content to nextflow.config

  GallVp

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  df008f4

• Now using a txt file for params.external_protein_fastas

  GallVp

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  92b3d2f

• Now using nf-validation for params.liftoff_annotations

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  8ffcc32

Commits on Mar 28, 2024

• Now using nf-validation for all the parameters

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  f028dcd

Commits on Apr 2, 2024

• Added MERGE_ANNOTATIONS sub-workflow

  GallVp

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  e931725

• Now merging with agat/spmergeannotations

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  40f5cc5

Commits on Apr 9, 2024

• Added GFF_EGGNOGMAPPER sub-workflow

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  47bb3ed

Commits on Apr 12, 2024

• Now using TSEBRA to purge models which do not have full intron support from BRAKER hints

  GallVp

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  662c4b1

• Updated modules and subworkflows

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  22e609c

• Updated eggnogmapper

  GallVp

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  f2d333c

• Patched eggnogmapper and gffread

  GallVp

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  3acaaac

• Added params eggnogmapper_evalue and eggnogmapper_pident

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  9915ee8

Commits on Apr 17, 2024

• Added PURGE_NOHIT_BRAKER_MODELS sub-workflow

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  0e5a43d

Commits on Apr 18, 2024

• Removed liftoff models with valid_ORF=False

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  f133453

• Now merging BRAKER and liftoff models before running eggnogmapper

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  999236d

• Added GFF_MERGE_CLEANUP sub-workflow

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  70898ca

Commits on Apr 22, 2024

• Now using description field to store notes and textual annotations in the gff files

  GallVp

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  8fc0958

Commits on Apr 23, 2024

• Added GFF_STORE sub workflow

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  57138fd

Commits on Apr 24, 2024

• Now using local tests/stub files for GitHub CI

  GallVp

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  fe6578f

• Updated flowchart

  GallVp

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  cc6f391

• Updated flowchart

  GallVp

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  92e7aff

• Updated flowchart

  GallVp

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  b553453

• Updated flowchart

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  20e6874

Commits on Apr 28, 2024

• Updated README

  GallVp

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  3b04340

• Now removing iso-forms left by TSEBRA using AGAT_SPFILTERFEATUREFROMKILLLIST

  GallVp

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  bffdb63

• Added pyproject.toml

  GallVp

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  099b76d

Commits on Apr 29, 2024

• Version bumped to 0.3.0

  GallVp

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  7e338d6

• Updated PFR params

  GallVp

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  53088d7

Commits on Apr 30, 2024

• Now using PFAMs from eggnog if description is '-'

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  d11f831