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Incorporate Feedback and fix typos#276

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SusiJo merged 13 commits intoqbic-pipelines:devfrom
SusiJo:fix_typos
May 30, 2025
Merged

Incorporate Feedback and fix typos#276
SusiJo merged 13 commits intoqbic-pipelines:devfrom
SusiJo:fix_typos

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@SusiJo SusiJo commented May 26, 2025 •
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PR checklist

Incorporated feedback from BioPM team. Also applied editorconfig rules to autoformat.
Removed parameter --path_quote as this is not used anymore.

  • 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).

SusiJo
SusiJo commented May 26, 2025
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Comment thread bin/Execute_report.R
SusiJo
SusiJo commented May 26, 2025
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Comment thread conf/modules.config
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SusiJo commented May 27, 2025

Also fixes the table of summary stats from multiqc
Table before fix:
Screenshot 2025-05-27 at 10 54 27

After fix:
Screenshot 2025-05-27 at 10 57 23

@SusiJo SusiJo requested a review from qbicStefanC May 27, 2025 09:24
famosab
famosab approved these changes May 28, 2025
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I think this looks good, just minor comments :)

Comment thread assets/rnadeseq_report.Rmd Outdated
Comment thread assets/rnadeseq_report.Rmd Outdated
Comment thread assets/rnadeseq_report.Rmd
qbicStefanC
qbicStefanC reviewed May 30, 2025
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Comment thread assets/rnadeseq_report.Rmd Outdated
qbicStefanC
qbicStefanC reviewed May 30, 2025
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Comment thread assets/rnadeseq_report.Rmd Outdated
qbicStefanC
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If we an address my two comments above , we are good to go. Checked most carefully the rmd file but also do find the options/parameters in the Execute report.R file now much more clear and better readable.

Comment thread assets/rnadeseq_report.Rmd Outdated
@SusiJo SusiJo merged commit 27d6ff9 into qbic-pipelines:dev May 30, 2025
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@SusiJo SusiJo mentioned this pull request May 30, 2025
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@SusiJo SusiJo deleted the fix_typos branch May 30, 2025 09:23
SusiJo added a commit that referenced this pull request Jul 3, 2025
@SusiJo
Release 2.6 (#279)
1311f0b 
* Add EnhancedVolcano (#267)

* add enh. volcano

* update docu

* add comment

* rm comments, add omitNa

* ch version to dev

* add volcano to tests

* fix deprecated key-value

* update docs,changelog

* prettier test rsem profile

* fix contrast names

* Apply color scheme of EnhancedVolcano to plotly volcano (#268)

* add colors to plotly volcano

* add color scale

* Hotfix colors volcano plot (#271)

* hotfix switch volcano colors

* fix colors

* add abs, rm space

* rm "feature" text

* update titles, legends

* add subtitle for interactive plot

* ch y-axis label

* rm outcommented lines

* Put gprofiler in tabs (#270)

* put gprofiler in tabs

* revert

* linting

* trim whitespace

* mod plot title

* Bugfixes pathway analysis (#273)

* raise max dimensions limit

* concat ensembl ids with gene names

* update changelog & usage

update changelog & usage

update changelog & usage

Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>

fix typo

* Update report (#275)

* change report name

* modify report

* update report & tests & fix volcano colors

* add to changelog, references

* fix citation

* fix df RIN

* fix linting & ci

* fix padding

* update md5sums due to sampleNames

* apply suggestions

* update confs

* apply suggestion

* add num all genes

* change icon

* adjust docs text

* Incorporate Feedback and fix typos (#276)

* incorporate feedback

* update report

* fix typos

* update changelog

* fix pre-commit

* fix spaces

* fix colored cells

* linting

* fix typos

* adjust table border

* fix typos

* apply suggestions

* apply suggestions

* Bugfix summary  (#278)

* fix contrast

* update usage

* add to changelog

* update test

* PR num

* ch md5sum

* Add gene biotypes to interactive volcano plots   (#272)

* adjust md5sums due to gtf biotypes

* update branch

* fix assignment

* add biotype to final DE table

* update md5sums

* version bump to 2.6 (#277)

* update branch.yml

* apply suggestion lint

* add to ignore

* update branch.yml

* test docker download

* rm pull_request_target rule

* update branch protection

* update branch protection

* update branch protection

* revert branch yml

* update branch yml

* test download

* test update

* update branch.yml

* change publishdir mode

* update version test

* Bugfix volcano (#280)

* fix thresholds in enhanced volcano

* add to changelog

* Prettify long contrast names in plot titles (#281)

* prettify long contrast names in plot titles

* add new test profile but not for ci

* rename files

* correct pr nums

* apply suggestions (#282)

* update env name

* revert download.yml

* test apptainer

* change order

* revert download.yml

* revert cachedir

* update md5sum

* Modify input base (#283)

* switch back to githubusercontent

* add to changelog
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@qbicStefanC qbicStefanC qbicStefanC approved these changes

@famosab famosab famosab approved these changes

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@SusiJo @qbicStefanC @famosab
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