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Release: 2.5.0 #524

Merged
merged 64 commits into from
Oct 10, 2023
Merged

Release: 2.5.0 #524

merged 64 commits into from
Oct 10, 2023

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jfy133
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@jfy133 jfy133 commented Oct 9, 2023

Almost exclusively bug fixes, but includes some deprecated/replaced parameters thus the larger version bump.

Added

  • #504 - New parameters --busco_db, --kraken2_db, and --centrifuge_db now support directory input of a pre-uncompressed database archive directory (by @gregorysprenger).

Changed

Fixed

  • #514 - Fix missing CONCOCT files in downstream output (reported by @maxibor, fix by @jfy133)
  • #515 - Fix overwriting of GUNC output directories when running with domain classification (reported by @maxibor, fix by @jfy133)
  • #516 - Fix edge-case bug where MEGAHIT re-uses previous work directory on resume and fails (reported by @husensofteng, fix by @prototaxites)
  • #520 - Fix missing Tiara output files (fix by @jfy133)
  • #522 - Fix 'nulls' in depth plot PNG files (fix by @jfy133)

Dependencies

Deprecated

  • #504 - --busco_reference, --busco_download_path, --save_busco_reference parameters have been deprecated and replaced with new parameters (by @gregorysprenger).

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/mag branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

gregorysprenger and others added 30 commits September 5, 2023 14:24
@gregorysprenger
handle local kraken2 db
328740c
@gregorysprenger
handle local centrifuge db
7f8909b
@gregorysprenger
use busco_db and handle local and downloaded tar.gz files
118271c
@gregorysprenger
update information about kraken, centrifuge, and busco databases
d4b6258
@gregorysprenger
update parameter handling
4304cf6
@gregorysprenger
set busco_db input as a path channel
190129e
@gregorysprenger
handle busco_db inputs and allow for busco to auto download lineages
1961247
@nf-core-bot
Template update for nf-core/tools version 2.10
b6d3e78
@jfy133
update changelog
b2df8da
@jfy133
Merge pull request #513 from nf-core/bump-version
41ec8d7 
Post 2.4.0 release version bump
@jfy133
Merge branch 'dev' into nf-core-template-merge-2.10
9b8ef78
@nf-core-bot
[automated] Fix linting with Prettier
58c4a38
@jfy133
fix dumpsoftwware hash
e2952b0
@jfy133
Comments after review
91744ec
@jfy133
Improve TODO
bee4749
@jfy133
Update CHANGELOG
3f64e92
@jfy133
Fix CONCOCT missing in some globs
0c7c31e
@jfy133
Update CHANGELOG
42d70e6
@jfy133
Fix directory names of GUNC output to prevent overwriting
8dfb907
@jfy133
Apply suggestions from code review
24fe29e
@jfy133
Update CHANGELOG
a2f6168
@jfy133
Update OUTPUT docs
5b4be5d
@jfy133
Merge pull request #511 from nf-core/nf-core-template-merge-2.10
62b2d1c 
Important! Template update for nf-core/tools v2.10
@jfy133
Merge branch 'dev' into fix-missing-concoct-globs
3943efa
@jfy133
Merge branch 'dev' into fix-gunc-overwriting
f0b09f5
@jfy133
Update docs/output.md
2db25be
@prototaxites
Update megahit.nf
e4860c4
@prototaxites
Update CHANGELOG.md
f994012
@jfy133
Merge pull request #514 from nf-core/fix-missing-concoct-globs
3cd0541 
Fix missing concoct globs
@jfy133
Merge branch 'dev' into fix-gunc-overwriting
f9691cf
jfy133 and others added 23 commits October 4, 2023 11:06
@jfy133
Update docs/output.md
90eb2cc
@jfy133
Apply suggestions from code review
3c1e286
@jfy133
Merge pull request #520 from nf-core/tiara-publish-fix
5ea7104 
Fix Tiara publishing files
@gregorysprenger
space needed for when adding to p var
e09c6a0
@gregorysprenger
fix busco directory handling and have consistency on channel vars
1f5d1a7
@gregorysprenger
harshil rule on emit lines
42b914d
@gregorysprenger
db_name has to be the same as centrifuge filenames
3521da0
@gregorysprenger
update changelog
04ceb89
@jfy133
Fix nulls in bin depths
d511ebd
@gregorysprenger @jfy133
fix spelling error
5cb4f41 
Co-authored-by: James A. Fellows Yates <[email protected]>
@gregorysprenger
use file attribute getBaseName
e4525bc
@gregorysprenger
revert back to only decompressing tar.gz files
0d84819
@gregorysprenger
handle centrifuge and kraken db parsing
10ae039
@jfy133
Merge pull request #522 from nf-core/fix-null-in-depths
04e2b57 
Fix null in depth PNG files
@gregorysprenger
less verbose way of checking multiple file extensions
e77e44d
@gregorysprenger
remove view function from channel
21fcad2
@gregorysprenger
use getSimpleName file attribute
55fd640
@gregorysprenger
update changelog
d122b49
@gregorysprenger
Merge branch 'dev' into add_local_db
a111ca8
@jfy133
Add depcrecateion and updated changed entries
f0e4ce6
@nf-core-bot
[automated] Fix linting with Prettier
6190222
@jfy133
Merge pull request #504 from gregorysprenger/add_local_db
86ce3d7 
Allow local databases to be used for kraken2, centrifuge, and busco
@jfy133
Update version for release
b3e5eec
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github-actions bot commented Oct 9, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b3e5eec

+| ✅ 157 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 2.5.0
  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file [TODO: try and test using for --host_fasta and --host_genome]
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in WorkflowMag.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-09 10:00:05

maxulysse
maxulysse approved these changes Oct 9, 2023
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LGTM

sguizard
sguizard approved these changes Oct 9, 2023
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LGTM

@jfy133
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jfy133 commented Oct 9, 2023

Just running one last test to see if I can get the AWS full tests working, if not I'll do the release, if yes will do a quick extra PR. Thanks both!

jfy133
jfy133 commented Oct 10, 2023
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@jfy133 jfy133 merged commit ba72349 into master Oct 10, 2023
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@jfy133 @maxulysse @sguizard @gregorysprenger @nf-core-bot @prototaxites