Code

nf-core 3.3.0 release#734

Code

Merged

jfy133 merged 108 commits intomasternf-core/mag:masterfrom devnf-core/mag:devCopy head branch name to clipboardDec 19, 2024

+8,712-1,726

Commits

Commits on Oct 14, 2024

• install chopper from nf-core/chopper

  muabnezor

  committed
  ad89172

  Copy full SHA for ad89172

• Add nanoq from nf-core/nanoq, and add code in longread_preprocessing subworkflow for alternative use of chopper for lambda-removal instead of nanolyse, and nanoq for longread filtering instead of f…

  Show description for c614c01
  muabnezor

  committed
  c614c01

  Copy full SHA for c614c01

• Fix config for modules nanoq and filtlong in modules.config

  muabnezor

  committed
  7102af4

  Copy full SHA for 7102af4

Commits on Oct 15, 2024

• Make it possible to use chopper as filtering tool as well

  muabnezor

  committed
  9bc8156

  Copy full SHA for 9bc8156

Commits on Oct 27, 2024

• feat: Migrate from CheckM to CheckM2

  Show description for 53864d2
  dialvarezs

  committed
  53864d2

  Copy full SHA for 53864d2

• fix: Bring back CheckM

  dialvarezs

  committed
  ca2f97b

  Copy full SHA for ca2f97b

• fix: One more thing

  dialvarezs

  committed
  05e3393

  Copy full SHA for 05e3393

• fix: Linting

  dialvarezs

  committed
  3e49dbf

  Copy full SHA for 3e49dbf

• fix: Option and checks in bin summary script

  dialvarezs

  committed
  b1b6518

  Copy full SHA for b1b6518

• Fix: missing import

  dialvarezs

  committed
  73b5794

  Copy full SHA for 73b5794

Commits on Oct 28, 2024

• docs: Output, changelog and citation for CheckM2

  dialvarezs

  committed
  325310b

  Copy full SHA for 325310b

• docs: readme

  dialvarezs

  committed
  b88302a

  Copy full SHA for b88302a

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

  dialvarezs

  committed
  d62a671

  Copy full SHA for d62a671

• docs: Update readme

  dialvarezs

  committed
  3da7441

  Copy full SHA for 3da7441

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

  Show description for 3d98415
  dialvarezs

  committed
  3d98415

  Copy full SHA for 3d98415

• fix: Restore mistakenly deleted code

  dialvarezs

  committed
  8b4fcc7

  Copy full SHA for 8b4fcc7

• Testing param

  dialvarezs

  committed
  6f38499

  Copy full SHA for 6f38499

• Complete schema description

  dialvarezs

  committed
  dca7b71

  Copy full SHA for dca7b71

• Fix channel

  dialvarezs

  committed
  dd7f135

  Copy full SHA for dd7f135

• Invert parameter

  dialvarezs

  committed
  705198e

  Copy full SHA for 705198e

Commits on Oct 29, 2024

• Merge branch 'dev' into add_chopper_nanoq

  jfy133

  authored
  59aa4ad

  Copy full SHA for 59aa4ad

Commits on Oct 30, 2024

• Apply suggestions from code review

  Show description for 9504788
  

  dialvarezs

  and

  jfy133

  authored
  9504788

  Copy full SHA for 9504788

• Update changelog

  dialvarezs

  committed
  af7300f

  Copy full SHA for af7300f

• Pre-commit

  dialvarezs

  committed
  aa25201

  Copy full SHA for aa25201

• Post patch bump

  jfy133

  committed
  8c46072

  Copy full SHA for 8c46072

• Apply suggestions from code review

  jfy133

  authored
  1a00c14

  Copy full SHA for 1a00c14

• Merge pull request #712 from nf-core/post-patch-bump

  Show description for f0ca539
  jfy133

  authored
  f0ca539

  Copy full SHA for f0ca539

• Merge pull request #708 from dialvarezs/dev-exclude-unbinned

  Show description for cd5ebae
  jfy133

  authored
  cd5ebae

  Copy full SHA for cd5ebae

Commits on Oct 31, 2024

• Bin QC workflow

  dialvarezs

  committed
  76dac5c

  Copy full SHA for 76dac5c

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

  dialvarezs

  committed
  0ebab07

  Copy full SHA for 0ebab07

• Cleanup

  dialvarezs

  committed
  38ce756

  Copy full SHA for 38ce756

• Final touches

  dialvarezs

  committed
  3702329

  Copy full SHA for 3702329

Commits on Nov 1, 2024

• Integrate GUNC in BIN_QC subworkflow

  dialvarezs

  committed
  0eb167a

  Copy full SHA for 0eb167a

• Code style improvements

  dialvarezs

  committed
  f0a6999

  Copy full SHA for f0a6999

• Update chopper module. Pass on fasta file when invoking chopper process

  muabnezor

  committed
  cce1ada

  Copy full SHA for cce1ada

• resolve merge conflicts

  muabnezor

  committed
  bfa5e06

  Copy full SHA for bfa5e06

• fix save_filtered_longreads parameter

  muabnezor

  committed
  7ec9a74

  Copy full SHA for 7ec9a74

• Update changelog, citations, and output

  muabnezor

  committed
  4ceacae

  Copy full SHA for 4ceacae

• Merge branch 'dev' into add_chopper_nanoq

  muabnezor

  authored
  4736487

  Copy full SHA for 4736487

• fix linting

  muabnezor

  committed
  03408c6

  Copy full SHA for 03408c6

• Merge remote-tracking branch 'origin/add_chopper_nanoq' into add_chopper_nanoq

  muabnezor

  committed
  a1f6ed7

  Copy full SHA for a1f6ed7

• move short read preprocessing into a subworkflow

  muabnezor

  committed
  4552dc7

  Copy full SHA for 4552dc7

Commits on Nov 22, 2024

• Update CHANGELOG.md

  Show description for fc9f7fc
  

  muabnezor

  and

  jfy133

  authored
  fc9f7fc

  Copy full SHA for fc9f7fc

• Update CHANGELOG.md

  Show description for 6e04c6e
  

  muabnezor

  and

  jfy133

  authored
  6e04c6e

  Copy full SHA for 6e04c6e

• Update conf/modules.config

  Show description for 6131b91
  

  muabnezor

  and

  jfy133

  authored
  6131b91

  Copy full SHA for 6131b91

• Update docs/output.md

  Show description for b7c88ea
  

  muabnezor

  and

  jfy133

  authored
  b7c88ea

  Copy full SHA for b7c88ea

• Update nextflow.config

  Show description for bd75811
  

  muabnezor

  and

  jfy133

  authored
  bd75811

  Copy full SHA for bd75811

• Update output.md

  muabnezor

  authored
  e978c23

  Copy full SHA for e978c23

• Merge pull request #692 from muabnezor/add_chopper_nanoq

  Show description for ebb4283
  muabnezor

  authored
  ebb4283

  Copy full SHA for ebb4283

Commits on Nov 23, 2024

• add include statements

  muabnezor

  committed
  00ac925

  Copy full SHA for 00ac925

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

  muabnezor

  committed
  65c8cea

  Copy full SHA for 65c8cea

• Fix multiqc input channel, channel mixing for short read processing is now handled in subworkflow

  muabnezor

  committed
  2768f5e

  Copy full SHA for 2768f5e

Commits on Nov 24, 2024

• Fix multiqc file mix

  muabnezor

  committed
  9a039da

  Copy full SHA for 9a039da

• Move assembly-input logic to main workflow

  muabnezor

  committed
  7861527

  Copy full SHA for 7861527

• Update Changelog

  muabnezor

  committed
  745a6c1

  Copy full SHA for 745a6c1

• remove include statements from main workflow

  muabnezor

  committed
  9273717

  Copy full SHA for 9273717

Commits on Nov 25, 2024

• Move assembly-input logic back into shortread subworkflow. Make sure to always declare the ch_short_reads_assembly even if assembly-input

  muabnezor

  committed
  16ba808

  Copy full SHA for 16ba808

• Merge branch 'dev' into dev-checkm2

  jfy133

  authored
  7e21b62

  Copy full SHA for 7e21b62

• Format include statements

  muabnezor

  committed
  f2507b2

  Copy full SHA for f2507b2

• Move assembly-input logic back to main workflow

  muabnezor

  committed
  0b3c9ba

  Copy full SHA for 0b3c9ba

Commits on Nov 27, 2024

• Address several review comments

  dialvarezs

  committed
  3158c52

  Copy full SHA for 3158c52

• Update modules

  dialvarezs

  committed
  6152696

  Copy full SHA for 6152696

• Make binqc_tool an input for BIN_SUMMARY

  dialvarezs

  committed
  ef1828c

  Copy full SHA for ef1828c

• Move bin qc database setup to the subworkflow

  dialvarezs

  committed
  bcae7f9

  Copy full SHA for bcae7f9

• Fix

  dialvarezs

  committed
  158ee12

  Copy full SHA for 158ee12

• Remove another it

  dialvarezs

  committed
  5738215

  Copy full SHA for 5738215

• Remove checkm/checkm2 ci tests

  dialvarezs

  committed
  49ebb71

  Copy full SHA for 49ebb71

Commits on Nov 28, 2024

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

  dialvarezs

  committed
  4ecd36f

  Copy full SHA for 4ecd36f

• Don't flatten bins for GUNC

  dialvarezs

  committed
  1cf1da7

  Copy full SHA for 1cf1da7

• Update changelog

  dialvarezs

  committed
  ea9075f

  Copy full SHA for ea9075f

• Emit bash version on busco_save_download

  dialvarezs

  committed
  a079596

  Copy full SHA for a079596

• Fix declaration

  dialvarezs

  committed
  80641b0

  Copy full SHA for 80641b0

Commits on Nov 29, 2024

• Remove unused bowtie2 multiqc channel

  muabnezor

  committed
  2262d60

  Copy full SHA for 2262d60

Commits on Dec 1, 2024

• Update checkm/qa module

  dialvarezs

  committed
  4b084b1

  Copy full SHA for 4b084b1

Commits on Dec 5, 2024

• Merge pull request #716 from muabnezor/shortread_subworkflow

  Show description for a9c213f
  muabnezor

  authored
  a9c213f

  Copy full SHA for a9c213f

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

  dialvarezs

  committed
  f75e9c4

  Copy full SHA for f75e9c4

• Handle skip_binqc properly

  dialvarezs

  committed
  d176fce

  Copy full SHA for d176fce

• Fix quoting and undercore unused variables

  dialvarezs

  committed
  3cfa020

  Copy full SHA for 3cfa020

Commits on Dec 9, 2024

• Fix parameter usage

  dialvarezs

  committed
  459274d

  Copy full SHA for 459274d

• Update README and CHANGELOG

  dialvarezs

  committed
  c7bec09

  Copy full SHA for c7bec09

Commits on Dec 10, 2024

• Fix input to single-end MEGAHIT runs

  jfy133

  committed
  1ef93a0

  Copy full SHA for 1ef93a0

• Update CHANGELOG.md

  jfy133

  authored
  3020a1c

  Copy full SHA for 3020a1c

Commits on Dec 11, 2024

• Address review comments

  dialvarezs

  committed
  3a38a37

  Copy full SHA for 3a38a37

Commits on Dec 12, 2024

• Template update for nf-core/tools version 3.1.0

  nf-core-bot

  committed
  a7fff01

  Copy full SHA for a7fff01

• Merge branch 'dev' into nf-core-template-merge-3.1.0

  jfy133

  authored
  dd0d44d

  Copy full SHA for dd0d44d

• Add contributors >1000 deleteion or addition LoC

  jfy133

  authored
  6abdfae

  Copy full SHA for 6abdfae

• Apply suggestions from code review

  jfy133

  authored
  6abebf4

  Copy full SHA for 6abebf4

Commits on Dec 13, 2024

• Merge pull request #724 from dialvarezs/fix-quotes

  Show description for 62d6f3d
  dialvarezs

  authored
  62d6f3d

  Copy full SHA for 62d6f3d

• Merge branch 'dev' into dev-checkm2

  jfy133

  authored
  009abd1

  Copy full SHA for 009abd1

• Update tests to integrate CheckM and CheckM2

  dialvarezs

  committed
  a2afa5e

  Copy full SHA for a2afa5e

• Fix for when checkm is not run for some bins

  dialvarezs

  committed
  61c23fe

  Copy full SHA for 61c23fe

• Merge pull request #707 from dialvarezs/dev-checkm2

  Show description for c096f9a
  dialvarezs

  authored
  c096f9a

  Copy full SHA for c096f9a

Commits on Dec 14, 2024

• Merge pull request #729 from nf-core/fix-megahit

  Show description for 7aebfa8
  sateeshperi

  authored
  7aebfa8

  Copy full SHA for 7aebfa8

• Re-add modules config loading

  jfy133

  authored
  b0475ff

  Copy full SHA for b0475ff

• Fix linting

  jfy133

  authored
  72a1037

  Copy full SHA for 72a1037

• Update CHANGELOG.md

  jfy133

  authored
  4a282ec

  Copy full SHA for 4a282ec

Commits on Dec 16, 2024

• Add support for prokka compliance mode

  jfy133

  committed
  dfa5c49

  Copy full SHA for dfa5c49

• Merge pull request #732 from nf-core/prokka-compliance

  Show description for 96f1e25
  jfy133

  authored
  96f1e25

  Copy full SHA for 96f1e25

• Update conf/modules.config

  jfy133

  authored
  5162787

  Copy full SHA for 5162787

• Merge pull request #731 from nf-core/nf-core-template-merge-3.1.0

  Show description for 2278c89
  jfy133

  authored
  2278c89

  Copy full SHA for 2278c89

• Bump version, update workflow diagram, export 300dpi logos

  jfy133

  committed
  a8b805e

  Copy full SHA for a8b805e

• [automated] Fix code linting

  nf-core-bot

  committed
  9598515

  Copy full SHA for 9598515

• Merge pull request #733 from nf-core/bump-version-for-release

  Show description for 0ba597c
  jfy133

  authored
  0ba597c

  Copy full SHA for 0ba597c

• Remove typo in parameter

  jfy133

  authored
  abcd63d

  Copy full SHA for abcd63d

• Apply suggestions from code review

  Show description for b0ed0c0
  

  jfy133

  and

  sateeshperi

  authored
  b0ed0c0

  Copy full SHA for b0ed0c0

Commits on Dec 17, 2024

• Add simplified metro map

  jfy133

  committed
  e571a28

  Copy full SHA for e571a28

Commits on Dec 19, 2024

• Update CHANGELOG.md

  jfy133

  authored
  3a39ca1

  Copy full SHA for 3a39ca1

• Update docs/output.md

  jfy133

  authored
  bde62aa

  Copy full SHA for bde62aa