Code

Release candidate for 0.6.0#129

Code

Merged

GallVp merged 42 commits intomainPlant-Food-Research-Open/genepal:mainfrom devPlant-Food-Research-Open/genepal:devCopy head branch name to clipboardDec 20, 2024

+2,767-131

Commits

Commits on Dec 4, 2024

• Add EXTRACT_CDS feature to GFF_STORE workflow

  liamlelievre

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• Update gff_store.nf

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• Update gff_store.nf

  liamlelievre

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• add EXTRACT_CDNA to gff_store.nf

  liamlelievre

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• add GFF_STORE:EXTRACT_CDNA to modules.config

  liamlelievre

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• Update gff_store.nf

  liamlelievre

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• Add cdna and cds outputs to output.md

  liamlelievre

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• Add notes about cdna and cds update to CHANGELOG.md

  liamlelievre

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• Added liamlelievre to contributors - README.md

  liamlelievre

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• Update output.md

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  liamlelievre

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• Added v0.6.0 notes to CHANGELOG.md

  liamlelievre

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• removed trailing whitespace gff_store.nf

  liamlelievre

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• Removed trailing whitespace - modules.config

  liamlelievre

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• rename params - modules.config

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  liamlelievre

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• Rename params - nextflow.config

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  liamlelievre

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• Added code contributors

  GallVp

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Commits on Dec 5, 2024

• Run nf-test successfully in minimal and stub

  

  liamlelievre

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• Run nf-test successfully in minimal and stub, renamed attr, updated docs

  

  liamlelievre

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• Merge branch 'main' into add-gffread-feature

  

  liamlelievre

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• Add attributes option for -F -D to cds and cdna

  

  liamlelievre

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• Fixed linting issues

  GallVp

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• Updated snapshot

  GallVp

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• Fixed nextflow-setup version

  GallVp

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• Fixed indent

  GallVp

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• Merge pull request #119 from liamlelievre/add-gffread-feature

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• Fixed an issue where TSEBRA failed because LIFTOFF lifted non-protein coding genes

  GallVp

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  fb9a0f4

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• Updated snapshots

  GallVp

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• Updated changelog

  GallVp

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• Merge pull request #122 from Plant-Food-Research-Open/patch/121

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Commits on Dec 10, 2024

• Fixed issues in genepal-report

  GallVp

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• Merge pull request #126 from Plant-Food-Research-Open/patch/124

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• Added parameter filter_genes_by_aa_length

  GallVp

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• Updated snapshots

  GallVp

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Commits on Dec 11, 2024

• Added test to verify that GFFREAD can filter mRNA by CDS length

  GallVp

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• Updated snapshots

  GallVp

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• Updated README and snapshot

  GallVp

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Commits on Dec 15, 2024

• Added 1 to filter_genes_by_aa_length to exclude stop codon from filter length

  GallVp

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• Merge pull request #127 from Plant-Food-Research-Open/feat/filter_genes_by_aa_length

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Commits on Dec 16, 2024

• Fixed post-liftoff merge

  GallVp

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• Merge pull request #130 from Plant-Food-Research-Open/fix/mergefail

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  GallVp

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Commits on Dec 19, 2024

• Fixed short intron crash

  GallVp

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Commits on Dec 20, 2024

• Merge pull request #131 from Plant-Food-Research-Open/fix/short_intron

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