Code

Release 0.6#112

Code

Merged

muffato merged 33 commits intomainsanger-tol/blobtoolkit:mainfrom devsanger-tol/blobtoolkit:devCopy head branch name to clipboardSep 13, 2024

+733-234

Commits

Commits on Aug 22, 2024

• Merge remote-tracking branch 'origin/main' into dev

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  40538b3

• Version bump

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  12a7557

• Directly query the NCBI API

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  bd2334e

• bugfix: Need all lineage names, not just eukaryotes

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  da7faf9

• Adding a parameter to choose the busco lineages

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  9c5b412

• Removed the legacy yaml configuration file

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• Generate a yaml file internally

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• Hide the CSV from the rest of the pipeline

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• Generate a more complete yaml to match the one we get from blobtoolkit

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• Update the database paths in the final meta.json

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• Fill in the reads too

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• Fill in the assembly information too

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• No need to generate the reference initial yaml file

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• Switched to the newer endpoint

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• Introduced --parameters to have flexibility regarding their order

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  e190bdd

• Adjust the taxon_id to make sure it exists in the NT database

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• All these parameters are mandatory

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  9963aa5

• bugfix: --busco is optional

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  e959c04

• bugfix: this should be a "path" so that the file is made available to the container

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  ed94111

• bugfix: accept older assembly versions

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  5962034

• These fields can be missing

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  121e372

• Some genomes don't have organelles

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  8085a74

• Easier to read

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• Release name

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• https://ncbiinsights.ncbi.nlm.nih.gov/2024/06/04/changes-ncbi-taxonomy-classifications/

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  8886dba

• Use GoaT in addition to the NCBI because GoaT also has the freshest ENA taxon_ids

  Show description for 70f961c
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  70f961c

• Added an option to skip filtering hits from the same species

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Commits on Aug 24, 2024

• Corrected the version as I want to be sure this is really ready for the big show

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  8c70c77

• Merge pull request #97 from sanger-tol/draft_assemblies

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  18d2daf

Commits on Sep 11, 2024

• Introduced the use_work_dir_as_temp parameter like in the other pipelines

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  152b773

• For large genomes, don't run Busco off /tmp

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• Getting ready for the release

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Commits on Sep 13, 2024

• Merge pull request #111 from sanger-tol/busco_tmp

  Show description for ca10b9b
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  ca10b9b