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Optimized outputs for PanKB + improvements to locus tag mapping

Pull request merge
pascalaldopushed 210 commits to main • 8165280…9852c0d • 
14 days ago

Optimized outputs for PanKB + improvements to locus tag mapping

pascalaldopushed 1 commit to feature_reorganize • bc067a6…4d50555 • 
on Jan 14

Some fixes

pascalaldopushed 1 commit to feature_reorganize • a8e1b5a…bc067a6 • 
on Nov 6, 2024

Forgot comma

pascalaldopushed 1 commit to feature_reorganize • 3cf7902…a8e1b5a • 
on Nov 5, 2024

Updated automlst_wrapper

pascalaldopushed 1 commit to feature_reorganize • 7791b83…3cf7902 • 
on Nov 5, 2024

Fix cd-hit version to mitigate roary error

pascalaldopushed 1 commit to feature_reorganize • 0816523…7791b83 • 
on Nov 5, 2024

Small fix

pascalaldopushed 1 commit to feature_reorganize • bd18622…0816523 • 
on Nov 3, 2024

Shift make_phylo_tree to merged gtdb+gtdbtk taxonomy

pascalaldopushed 1 commit to feature_reorganize • 7a85cfb…bd18622 • 
on Nov 3, 2024

Removed {stage} from ncbi_datasets

pascalaldopushed 1 commit to feature_reorganize • e883a12…7a85cfb • 
on Nov 3, 2024

Fixed erroneous correction

pascalaldopushed 1 commit to feature_reorganize • 046b4d0…e883a12 • 
on Nov 2, 2024

Fix in ncbi_annotation_datasets

pascalaldopushed 1 commit to feature_reorganize • 6d0a33c…046b4d0 • 
on Nov 2, 2024

Improvements

pascalaldopushed 1 commit to feature_reorganize • bef0417…6d0a33c • 
on Oct 30, 2024

Handle missing gff files

pascalaldopushed 1 commit to feature_reorganize • a7aeb1e…bef0417 • 
on Oct 28, 2024

Some small fixes and improvements for species with a large amount of …

pascalaldopushed 1 commit to feature_reorganize • fbd1d2e…a7aeb1e • 
on Oct 28, 2024

gtdbtk fix

pascalaldopushed 1 commit to feature_reorganize • 4162487…fbd1d2e • 
on Oct 24, 2024

Introduction of original locus tag mapping and iModulonDB interoperab…

pascalaldopushed 1 commit to feature_reorganize • 1a1b522…4162487 • 
on Oct 24, 2024

Small fixes + introduction of pankb_nova genome script

pascalaldopushed 1 commit to feature_reorganize • 8a3e395…1a1b522 • 
on Oct 22, 2024

Fixed that ln -s expects path relative to output file

pascalaldopushed 1 commit to feature_reorganize • 07acca0…8a3e395 • 
on Oct 21, 2024

Small change for testing

pascalaldopushed 1 commit to feature_reorganize • bca6e5e…07acca0 • 
on Oct 21, 2024

Improvements

pascalaldopushed 1 commit to feature_reorganize • ce75758…bca6e5e • 
on Oct 21, 2024

Intoduces pankb_nova scripts

pascalaldopushed 1 commit to feature_reorganize • afe43f2…ce75758 • 
on Oct 17, 2024

New minimal PanKB workflow

pascalaldopushed 1 commit to feature_reorganize • e02da71…afe43f2 • 
on Oct 7, 2024

Another fix

pascalaldopushed 1 commit to feature_reorganize • d7addf1…e02da71 • 
on Oct 7, 2024

Small fix

pascalaldopushed 1 commit to feature_reorganize • 2ac9a5b…d7addf1 • 
on Oct 7, 2024

Enable a simplified variant of hte PanKB_Family workflow

pascalaldopushed 1 commit to feature_reorganize • 0d47120…2ac9a5b • 
on Oct 7, 2024

Add additional info to species summary

pascalaldopushed 1 commit to feature_reorganize • 94c74eb…0d47120 • 
on Oct 7, 2024

Updated pankb_data_prep heatmap

pascalaldopushed 1 commit to feature_reorganize • 3d376f7…94c74eb • 
on Oct 4, 2024

small fix

pascalaldopushed 1 commit to feature_reorganize • 9926114…3d376f7 • 
on Oct 4, 2024

Create simple ncbi_meta based on assembly reports

pascalaldopushed 1 commit to feature_reorganize • 5670030…9926114 • 
on Oct 4, 2024

Added species_info to pankb_data_prep genome_page

pascalaldopushed 1 commit to feature_reorganize • 845f389…5670030 • 
on Oct 4, 2024