Emit both png and pdf plots in deseq2
#9654
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pinin4fjords
requested changes
Jan 20, 2026
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sorry, if we're going to have 'dispersion_plot_pdf', maybe the original should be 'dispersion_plot_png'?
…module operation (nf-core#9698) fix(mitohifi): update mitohifi to version topics, add a log file output, and change input processing to allow multiple input files
* Update seqtk/* version number collection for nf-core 3.5 * Update seqtk/* version number collection in subworkflows for nf-core 3.5 * Changed code for adjusting 3.5.0 * Changed code for adjusting 3.5.0 * Due to changes in /tseemann/barrnap * changed expression in version detection sed $(git grep -l grep) -i -e "s/grep Version | //" -e "s/ sed/ sed -n/" -e"s/Version/^Version/" -e"s,sion: //,sion: //p," * updated snapshot of fasta_hmmsearch_rank_fastas * Update samtools/bgzip version number collection for nf-core 3.5 --------- Co-authored-by: Takii-Fujita <takahiro-fujita@oist.jp> Co-authored-by: Charles Plessy <charles.plessy@oist.jp>
…nf-core#9691) * Add new input channel for premade seqid2map file * Add extra tests for using custom seqid2map file * Apply suggestions from code review * Update modules/nf-core/kraken2/build/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Allow more flexible database input using `find` to locate dmnd file * Replace broken download module with NXF download and untar * Also replace galah test * Fix path to script * Update main.nf.test * Update modules/nf-core/checkm2/predict/tests/main.nf.test * Update modules/nf-core/galah/tests/main.nf.test * Fix test code --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
* strict syntax + versions topic * simplified eval for versions and added ontologies
* snapshots * fix meta + snapshots * reports-> multiqc_files * add task.process * fix snapshots
* Update container image URL for localcdsearch * Update container URL for localcdsearch module
* initial stage commit for samtools quickcheck * fix tests * update tests * fix meta * changed module objective: returns exit code env * fix linter shenanigans * change description of EXIT_CODE return type * more negative tests * correcting Bad header test case * adding htslib for good practice
…atrix with `dream` (nf-core#9675) * Bugfix: Generate dream normalised matrix only once * Update snapshot * Voom can only work with 1 thread * Fix parallel execution of voom * Fix ext.when configuration * Remove `ext.when` declarations
pinin4fjords
approved these changes
Jan 20, 2026
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PR checklist
Closes nf-core/differentialabundance#588
topic: versions- See version_topicslabelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda