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Release 2.2.0 #154

Merged
merged 36 commits into from
Aug 27, 2024
Merged

Release 2.2.0 #154

merged 36 commits into from
Aug 27, 2024

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Lucpen
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@Lucpen Lucpen commented Aug 23, 2024

PR checklist

  • Release 2.2.0
  • 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
  • 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).

Lucpen and others added 30 commits June 28, 2024 12:26
@Lucpen
Merge pull request #143 from genomic-medicine-sweden/master
00e5eb3 
Merge pull request #142 from genomic-medicine-sweden/dev
feat added possibility to download refs
2d90721
linitng
43ea83a
fix linting
05ebdaf
fix linting
50c7b5d
fix channels
3e5e6d8
@Lucpen
Update CHANGELOG.md
0508398
fix wget_download
3271cd5
@Lucpen
fix bootstrapann
946f311
@Lucpen
fix bootstrapann
72cfeab
@Lucpen
Update CHANGELOG.md
9e4decc
@Lucpen
Update CHANGELOG.md
096719d
@Lucpen
Update CHANGELOG.md
3ec8f26
@Lucpen @fellen31
Update CHANGELOG.md
a353c5c 
Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com>
@Lucpen
Merge pull request #151 from genomic-medicine-sweden/fix_bootstrapann
407e782 
fix bootstrapann input
@Lucpen
Merge branch 'dev' into download_references2
5b48060
@Lucpen @jemten
Apply suggestions from code review
bfd8376 
Co-authored-by: Anders Jemt <jemten@users.noreply.github.com>
@Lucpen
Apply suggestions from code review
3898fd5
@Lucpen @jemten
Apply suggestions from code review
cc675f4 
Co-authored-by: Anders Jemt <jemten@users.noreply.github.com>
fix modules/local/wget_download.nf
24b3c5b
fix output vep_to_download
e510080
fix build_vep_cache
dd83bdc
avoid publishing of wget and gnomad_download modules
c49d4c3
avoid publishing of wget and gnomad_download modules
173cb2b
@Lucpen
Merge pull request #149 from genomic-medicine-sweden/download_referen…
f87da99 
…ces2

Added possibility to download refs
update modules
c412eb4
bump to version 2.20
d4ac03b
updated changelog
376ce25
@Lucpen
Update CHANGELOG.md
3742b1a
@Lucpen
Merge pull request #153 from genomic-medicine-sweden/prepare_release_…
b5ad8a1 
…2.2.0

Prepare release 2.2.0
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github-actions bot commented Aug 23, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 896292d

+| ✅ 166 tests passed       |+
#| ❔ 317 tests were ignored |#
!| ❗   9 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • nextflow_config - Config manifest.version should end in dev: 2.2.0
  • 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 ci.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-27 07:06:36

@Lucpen Lucpen requested a review from jemten August 23, 2024 12:24
@Lucpen Lucpen marked this pull request as ready for review August 23, 2024 12:24
@Lucpen Lucpen requested a review from a team as a code owner August 23, 2024 12:24
@Lucpen Lucpen added the Ready for review Ready for review label Aug 23, 2024
Lucpen
Lucpen commented Aug 26, 2024
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fellen31
fellen31 requested changes Aug 26, 2024
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Nice work!

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@Lucpen @fellen31
Apply suggestions from code review
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Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com>
Lucpen
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@Lucpen Lucpen requested a review from fellen31 August 26, 2024 16:47
Lucpen
Lucpen commented Aug 27, 2024
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@Lucpen Lucpen merged commit 0e7c4c9 into master Aug 27, 2024
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Lucpen added a commit that referenced this pull request Aug 27, 2024
@Lucpen
Merge pull request #155 from genomic-medicine-sweden/master
a35dcb0 
Merge pull request #154 from genomic-medicine-sweden/dev
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@fellen31 fellen31 fellen31 approved these changes

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