Update report#275
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SusiJo merged 15 commits intoqbic-pipelines:devfrom May 23, 2025
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d4straub
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Looks nice, I have a few comments though.
This was referenced May 23, 2025
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* 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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PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).