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Release 2.5 #257

Merged
merged 37 commits into from
Dec 13, 2024
Merged

Release 2.5 #257

merged 37 commits into from
Dec 13, 2024

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WackerO
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@WackerO WackerO commented Dec 12, 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
  • 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).

WackerO and others added 30 commits August 2, 2024 13:43
@WackerO
fixed contrast pairs, updated changelog
46f8902
@WackerO @skrakau
Update CHANGELOG.md
87304f0 
Co-authored-by: Sabrina Krakau <[email protected]>
@WackerO
Added separate param for setting qval threshold for pathway analysis
02fc8ff
@qbicStefanC
Get raw gene count tables from either Salmon and RSEM analysis
bf35b0f 
Update RNAseq_report.Rmd
@qbicStefanC
Update RNAseq_report.Rmd
750278b
@WackerO
Fixed bug with github actions
a601e22
@WackerO
update changelog
3efd687
@WackerO
Merge pull request #250 from WackerO/contrast_pairs
eeda61e 
Fix contrast pairs
@WackerO
Merge branch 'dev' of https://github.com/qbic-pipelines/rnadeseq into…
fc0591d 
… dev
@WackerO
Merge pull request #252 from WackerO/dev
d904f4b 
Fixed bug with github actions
@WackerO
Fixed pval format in report, added test
5f23f54
@WackerO
updated test yml
4c57882
@WackerO
changed test threshold
1e8f63b
@WackerO
updated test.yml
9065188
@WackerO
renamed param, updated threshold
f6e4db0
@WackerO
Merge pull request #253 from WackerO/enrich_qval
8a3e561 
Added separate param for setting adjusted pval threshold for pathway analysis
@qbicStefanC
Update test_star_salmon.yml
9e1c23e 
Added file path and checksum for raw_gene_counts.tsv file
@qbicStefanC
Update test_star_rsem.yml
4fc1d15 
Added file path and checksum for raw_gene_counts.tsv file
@qbicStefanC
Update CHANGELOG.md
322d388 
added PR #251 Get raw gene count tables from either Salmon and RSEM analysis
@qbicStefanC
Update CHANGELOG.md
4e2cdba
@qbicStefanC
Update CHANGELOG.md
18d1684
@qbicStefanC
Update CHANGELOG.md
71f1c38
@qbicStefanC
Merge branch 'dev' into master
324f613
@WackerO
Update assets/RNAseq_report.Rmd
c82108d
@WackerO
Update assets/RNAseq_report.Rmd
0e1f27e
@WackerO
Update CHANGELOG.md
e20c2b9
@WackerO
Merge pull request #251 from qbicStefanC/master
61e9b24 
Get raw gene count tables from either Salmon and RSEM analysis
@WackerO
Updated usage docs with missing params
cb00305
@WackerO
Added trycatch to enrichment plots
8bc2a77
@WackerO
prettier
0c6a3cd
WackerO and others added 3 commits December 9, 2024 11:42
@WackerO
prettier
8a994ad
@WackerO
Merge pull request #255 from WackerO/dev
5a819f8 
Add missing params to usage docs
@WackerO
Merge pull request #256 from WackerO/trycatch_enrich
7eeee20 
Add trycatch to enrichment plots
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This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @WackerO,

It looks like this pull-request is has been made against the qbic-pipelines/rnadeseq master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the qbic-pipelines/rnadeseq dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

tillenglert
tillenglert approved these changes Dec 12, 2024
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I left some comments, otherwise LGTM! 🚀

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mapo9
mapo9 approved these changes Dec 13, 2024
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lgtm! 🥇

bin/Execute_report.R Outdated Show resolved Hide resolved
@WackerO
fix stuff before release (add default description of pathway_adj_pval…
9f9d30e 
…_threshold, remove excessive logic of the param
@WackerO WackerO mentioned this pull request Dec 13, 2024
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WackerO commented Dec 13, 2024

Many thanks guys!

@WackerO WackerO merged commit e53bbae into master Dec 13, 2024
29 of 36 checks passed
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@tillenglert tillenglert tillenglert approved these changes

@mapo9 mapo9 mapo9 approved these changes

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@WackerO @mapo9 @tillenglert @qbicStefanC