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Merging Feat/selection#23

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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

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Commits on Mar 20, 2024

• Updated modules and subworkflows

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• Now tracking liftoff from nf-core/modules

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Commits on Mar 21, 2024

• Added before

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• Lightweight stub test and removed file.simpleName bug

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Commits on Mar 24, 2024

• Now using 1 round for augustus training for test data

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Commits on Mar 25, 2024

• Now braker can be skipped by providing braker files

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• Added gffcompare to merge liftoff annotations

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• Renamed samplesheet param to fastq

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Commits on Mar 26, 2024

• Now using assemblysheet for inputs

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Commits on Mar 27, 2024

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

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

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• Now using a txt file for params.external_protein_fastas

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• Now using nf-validation for params.liftoff_annotations

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Commits on Mar 28, 2024

• Now using nf-validation for all the parameters

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Commits on Apr 2, 2024

• Added MERGE_ANNOTATIONS sub-workflow

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• Now merging with agat/spmergeannotations

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Commits on Apr 9, 2024

• Added GFF_EGGNOGMAPPER sub-workflow

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Commits on Apr 12, 2024

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

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• Updated modules and subworkflows

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  22e609c

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• Updated eggnogmapper

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• Patched eggnogmapper and gffread

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• Added params eggnogmapper_evalue and eggnogmapper_pident

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Commits on Apr 17, 2024

• Added PURGE_NOHIT_BRAKER_MODELS sub-workflow

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Commits on Apr 18, 2024

• Removed liftoff models with valid_ORF=False

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• Now merging BRAKER and liftoff models before running eggnogmapper

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• Added GFF_MERGE_CLEANUP sub-workflow

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Commits on Apr 22, 2024

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

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Commits on Apr 23, 2024

• Added GFF_STORE sub workflow

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Commits on Apr 24, 2024

• Now using local tests/stub files for GitHub CI

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  fe6578f

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• Updated flowchart

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  cc6f391

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• Updated flowchart

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  92e7aff

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• Updated flowchart

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• Updated flowchart

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Commits on Apr 28, 2024

• Updated README

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• Now removing iso-forms left by TSEBRA using AGAT_SPFILTERFEATUREFROMKILLLIST

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• Added pyproject.toml

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Commits on Apr 29, 2024

• Version bumped to 0.3.0

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  7e338d6

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• Updated PFR params

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Commits on Apr 30, 2024

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

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