Code

Bin QC Improvements#707

Code

Open

dialvarezs wants to merge 35 commits intonf-core:devnf-core/mag:devfrom dialvarezs:dev-checkm2dialvarezs/mag:dev-checkm2Copy head branch name to clipboard

+1,845-563

Commits

Commits on Oct 27, 2024

• feat: Migrate from CheckM to CheckM2

  Show description for 53864d2
  dialvarezs

  committed
  53864d2

• fix: Bring back CheckM

  dialvarezs

  committed
  ca2f97b

• fix: One more thing

  dialvarezs

  committed
  05e3393

• fix: Linting

  dialvarezs

  committed
  3e49dbf

• fix: Option and checks in bin summary script

  dialvarezs

  committed
  b1b6518

• Fix: missing import

  dialvarezs

  committed
  73b5794

Commits on Oct 28, 2024

• docs: Output, changelog and citation for CheckM2

  dialvarezs

  committed
  325310b

• docs: readme

  dialvarezs

  committed
  b88302a

• Merge remote-tracking branch 'upstream/dev' into dev-checkm2

  dialvarezs

  committed
  d62a671

• docs: Update readme

  dialvarezs

  committed
  3da7441

• refactor: Merge checkm and checkm2 subworkflows in a single one

  Show description for 3d98415
  dialvarezs

  committed
  3d98415

• fix: Restore mistakenly deleted code

  dialvarezs

  committed
  8b4fcc7

Commits on Oct 31, 2024

• Bin QC workflow

  dialvarezs

  committed
  76dac5c

• Merge remote-tracking branch 'upstream/dev' into dev-checkm2

  dialvarezs

  committed
  0ebab07

• Cleanup

  dialvarezs

  committed
  38ce756

• Final touches

  dialvarezs

  committed
  3702329

Commits on Nov 1, 2024

• Integrate GUNC in BIN_QC subworkflow

  dialvarezs

  committed
  0eb167a

• Code style improvements

  dialvarezs

  committed
  f0a6999

Commits on Nov 25, 2024

• Merge branch 'dev' into dev-checkm2

  jfy133

  authored
  7e21b62

Commits on Nov 27, 2024

• Address several review comments

  dialvarezs

  committed
  3158c52

• Update modules

  dialvarezs

  committed
  6152696

• Make binqc_tool an input for BIN_SUMMARY

  dialvarezs

  committed
  ef1828c

• Move bin qc database setup to the subworkflow

  dialvarezs

  committed
  bcae7f9

• Fix

  dialvarezs

  committed
  158ee12

• Remove another it

  dialvarezs

  committed
  5738215

• Remove checkm/checkm2 ci tests

  dialvarezs

  committed
  49ebb71

Commits on Nov 28, 2024

• gtdbtk: add check when params.busco_db is not defined

  dialvarezs

  committed
  4ecd36f

• Don't flatten bins for GUNC

  dialvarezs

  committed
  1cf1da7

• Update changelog

  dialvarezs

  committed
  ea9075f

• Emit bash version on busco_save_download

  dialvarezs

  committed
  a079596

• Fix declaration

  dialvarezs

  committed
  80641b0

Commits on Dec 1, 2024

• Update checkm/qa module

  dialvarezs

  committed
  4b084b1

Commits on Dec 5, 2024

• Merge remote-tracking branch 'upstream/dev' into dev-checkm2

  dialvarezs

  committed
  f75e9c4

• Handle skip_binqc properly

  dialvarezs

  committed
  d176fce

Commits on Dec 11, 2024

• Address review comments

  dialvarezs

  committed
  3a38a37