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Migrate BUSCO to nf-core module#730

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dialvarezs wants to merge 29 commits intonf-core:devnf-core/mag:devfrom dialvarezs:dev-buscodialvarezs/mag:dev-buscoCopy head branch name to clipboard

+1,866-710

Commits

Commits on Dec 12, 2024

• Migrate to nf-core BUSCO module (WIP)

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  f85d7b0

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• Several busco-related fixes

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  25b72f1

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• More fixes

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  db88a3c

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• Fixes in combine_tables script

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  091a54a

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• Add more cpus to busco, and fix comparison in combine_tables

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  4a22358

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• Exclude failed BUSCO bins from GTDB-Tk, update changelog

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  bd22078

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• Save busco downloaded db

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  9512e95

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• Remove 'BUSCO_SAVE_DOWNLOAD' from conf/modules

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  9cc1d74

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Commits on Dec 15, 2024

• Merge remote-tracking branch 'upstream/dev' into dev-busco

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  46d19b1

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• Merge cleanup and fixes

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  edf4192

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• Define busco_lineage

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  6f200ef

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• Updade nf-core busco module

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  9702a87

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• Remove unneded config

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  abc1760

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Commits on Dec 16, 2024

• Fix busco channels and namespace in summary script

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  a44eb56

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Commits on Jan 2, 2025

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

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  37dbeed

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• Merge remote-tracking branch 'upstream/dev' into dev-busco

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  53dc7d3

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• Replace local combine_tsv module by nf-core csvtk/concat

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  eed82db

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• Fix changelog

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  299ff59

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• Update nf-core checkm2/databasedownload

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  89c7455

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• Fix tiara

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  c1d0552

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• Linting fixes

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  0b81462

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• Add ids to channel used by CONCAT_BINQC_TSV

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  f93e007

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Commits on Jan 8, 2025

• Update csvtk/concat module

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  07905a8

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• Fix gtdb usage of qc summary

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  1671aca

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• Update tests to bacteria odb12

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  3d4ba8b

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• Last fixes to get gtdb and bin summary working

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  d60ae40

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• Fix comment

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  135e703

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• busco_clean deprecation cleanup

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  44306da

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• Minor busco tweaks

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  f71249b

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