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Patch release 3.0.2 for fixing BUSCO, CONCOCT and Docker container errors #635

Merged
merged 23 commits into from
Jul 4, 2024
Merged

Patch release 3.0.2 for fixing BUSCO, CONCOCT and Docker container errors #635

merged 23 commits into from
Jul 4, 2024

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jfy133
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@jfy133 jfy133 commented Jun 28, 2024

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>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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).

jfy133 added 19 commits June 10, 2024 16:27
@jfy133
Post release version bump
d3b3d27
@jfy133
Merge pull request #629 from nf-core/dump-version-post
4136079 
Post release version bump
@jfy133
Get BUSCO to use --offline mode if a database is supplied
ec7eda6
@jfy133
Formatting
b5b98a1
@jfy133
Update CONCOCT workflow to remove mismatch
b324554
@jfy133
Add cGHANGELGO
47a9cf9
@jfy133
Replace PORECHOP with official module
d6d8fee
@jfy133
Update CHANGELOG.md
32ba76c
@jfy133
Bump nanoplot version 1.41.6 for valid docker container
5e45205
@jfy133
Remove some old local modules
b45d57a
@jfy133
update NanoLyse module
4bf4610
@jfy133
Output docs update
42db409
@jfy133
Merge pull request #632 from nf-core/general-container-updates-docker…
f52cbd3 
…-manifest

Fix: container updates docker manifest issues
@jfy133
Merge branch 'dev' into concoct-updates
d00722d
@jfy133
Merge branch 'dev' into busco-offline
2d1b0bb
@jfy133
Merge pull request #633 from nf-core/busco-offline
8b5f6a7 
Change BUSCO to run in offline mode when database already downloaded
@jfy133
Merge pull request #631 from nf-core/concoct-updates
5ea91e2 
Update CONCOCT workflow to remove mismatch failure and update container to fix slow single-threaded CONCOCT
@jfy133
Bump versions for patch release
faf2196
@jfy133
Merge pull request #634 from nf-core/patch-release-bump
74f7913 
Bump versions for patch release
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github-actions bot commented Jun 28, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4e12465

+| ✅ 306 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   6 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 3.0.2
  • 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 main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • 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

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-07-04 06:37:30

jfy133
jfy133 commented Jul 1, 2024
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prototaxites
prototaxites approved these changes Jul 1, 2024
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LGTM! 👍

mashehu
mashehu approved these changes Jul 3, 2024
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christopher-hakkaart
christopher-hakkaart approved these changes Jul 3, 2024
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Looks good 👍

@jfy133 @mashehu
Update CHANGELOG.md
c4ae311 
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
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jfy133 commented Jul 4, 2024

Thank you @prototaxites @mashehu @christopher-hakkaart !

jfy133
jfy133 commented Jul 4, 2024
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@jfy133 jfy133 merged commit bb74c46 into master Jul 4, 2024
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@maxibor maxibor mentioned this pull request Jul 4, 2024
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@mashehu mashehu mashehu approved these changes

@prototaxites prototaxites prototaxites approved these changes

@christopher-hakkaart christopher-hakkaart christopher-hakkaart approved these changes

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@jfy133 @mashehu @prototaxites @christopher-hakkaart