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New features and bug fixes #1

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Lfulcrum
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@Lfulcrum Lfulcrum commented Jan 6, 2025

Various code changes including:

  • Allow relative paths as inputs
  • Improve phylogenetic analysis workflow (allow different models and use SNP sites)
  • Allow bakta annotation (not extensively tested!)
  • Allow arbitary nf-core profiles to be used
  • Allow running with docker
  • Amend README

@Lfulcrum
Tidy up whitespace
188a657
@Lfulcrum
Cover all param cases for mytree and mygff
ccbd77d
@Lfulcrum
Refactor tree and annotation building
65f6c34
@Lfulcrum
Fix whitespace and improve validation
85901da
@Lfulcrum
Tidy up GWAS approaches and kmer annotation workflows
946bddf
@Lfulcrum
Relocate help message printing code
5356738
@Lfulcrum
Fix channel inputs
4964dbc
@Lfulcrum
Minor whitespace fix
5938bda
@Lfulcrum
Update panaroo image
d62d89c
@Lfulcrum
Fix unitig caller input
2a0e899
@Lfulcrum
Update phylogenetic analysis workflow
f4b63a7
@Lfulcrum
Make changes to README.md
7351225
@Lfulcrum
Use nf-core profile inheritance
099268f
@Lfulcrum
Comment on default executor
50cf7ff
@Lfulcrum
Update README.md
3f5d2ca
@Lfulcrum
Add support for docker profile
620683f
@Lfulcrum
Clarify pipeline requirements
d9a858f
@Lfulcrum
Amend credits
63cf92a
@Lfulcrum
Add pyseer Dockerfile
3e1d6e5
@Lfulcrum
Update docker URL for Pyseer image
7a33733
@Lfulcrum
Tweak README.md
20ab1eb
@Lfulcrum
Slim IQTree description
bfd5aa0
@Lfulcrum
Minor fixes to WriteReferenceText
9c61108
@Lfulcrum
Add bakta module
f0237b6
@Lfulcrum
Add bakta option
983bd81
@Lfulcrum
Use older bakta image to test db
9df44b2
@Lfulcrum
Fix bakta output
10aa093
@Lfulcrum
Stage gff files to make more suffix-agnostic
82133ee
@Lfulcrum
Allow memory to scale exponentially
87f0909
@Lfulcrum Lfulcrum requested a review from RosiTea January 6, 2025 14:49
RosiTea
RosiTea approved these changes Jan 6, 2025
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Thank you so much Will! Great stuff!!

@RosiTea
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RosiTea commented Jan 6, 2025

I see that you updated Panaroo to v.1.5.1 and added Bakta, fantastic! Just to note that we can update corresponding descriptions in README.md as well.

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@RosiTea RosiTea RosiTea approved these changes

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