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Patch release #174

Merged
merged 37 commits into from
Jul 23, 2024
Merged

Patch release #174

merged 37 commits into from
Jul 23, 2024

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LaurenceKuhl
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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/crisprseq 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).

LaurenceKuhl and others added 23 commits June 21, 2024 08:33
@LaurenceKuhl
Bump version
8e9c4c0
@LaurenceKuhl
Co-authored-by: Júlia Mir Pedrol <[email protected]>
421e61d
@LaurenceKuhl
Ran prettier
974eeec
@LaurenceKuhl
Merge branch 'dev' into dev
6cd7173
@LaurenceKuhl @mirpedrol
Update CHANGELOG.md
5015209 
Co-authored-by: Júlia Mir Pedrol <[email protected]>
@LaurenceKuhl
Merge pull request #159 from LaurenceKuhl/dev
c043710 
Bump dev version to 2.3.0dev
@LaurenceKuhl
Fix singularity image in mageckflute
720df97
@LaurenceKuhl
Merge branch 'dev' into dev
aa03c82
@mirpedrol
Merge pull request #160 from LaurenceKuhl/dev
0f7bd02 
Fix mageckflute container link for singularity
@mirpedrol
skip dolar signs on containerOptions
3005972
@mirpedrol
update changelog
3e1e21f
@mirpedrol
Merge pull request #163 from mirpedrol/skip-dolar-signs
5ca8c65 
skip dolar signs on containerOptions
@mashehu
add file names to code examples
8136045
@mirpedrol
remove patterns from correct_insertion_vc
792661b
@mashehu
Merge pull request #169 from mashehu/update-file-refs
d94bab6 
add file names to code examples
@mirpedrol
update changelog
42b1fc0
@mirpedrol
Merge pull request #170 from mirpedrol/r-script-bug
a4e18cf 
remove patterns from correct_insertion_vc
@LaurenceKuhl
Fix MAGeCKFlute error
bd3a824
@LaurenceKuhl
Update changelog
08348dc
@LaurenceKuhl @mashehu
Update templates/template_fluteMLE.R
4cc3b5b 
Co-authored-by: Matthias Hörtenhuber <[email protected]>
@LaurenceKuhl @mashehu
Update templates/template_fluteMLE.R
9f6298c 
Co-authored-by: Matthias Hörtenhuber <[email protected]>
@LaurenceKuhl
Merge pull request #171 from LaurenceKuhl/dev
2fe2b54 
Skip MAGeCKFlute function when error within package
@LaurenceKuhl
Update changelog for patch release
d18b4dd
LaurenceKuhl
LaurenceKuhl commented Jul 18, 2024
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github-actions bot commented Jul 18, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f50469c

+| ✅ 222 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 2.2.1
  • 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 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!

❔ Tests ignored:

  • files_exist - File is ignored: conf/test.config
  • files_exist - File is ignored: conf/test_full.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-07-23 10:21:03

@LaurenceKuhl
Merge pull request #175 from LaurenceKuhl/dev
8b9d040 
Update patch release name
mirpedrol
mirpedrol reviewed Jul 18, 2024
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mirpedrol
mirpedrol reviewed Jul 18, 2024
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mashehu
mashehu approved these changes Jul 23, 2024
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JoseEspinosa
JoseEspinosa approved these changes Jul 23, 2024
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LGTM 🚀

@mirpedrol @mashehu
Update CHANGELOG.md
f50469c 
Co-authored-by: Matthias Hörtenhuber <[email protected]>
@LaurenceKuhl LaurenceKuhl merged commit b2c583a into master Jul 23, 2024
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@mirpedrol mirpedrol mirpedrol left review comments

@JoseEspinosa JoseEspinosa JoseEspinosa approved these changes

@mashehu mashehu mashehu approved these changes

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@LaurenceKuhl @mashehu @JoseEspinosa @mirpedrol