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Fix abundance_differential_filter to only generate one normalized matrix with dream #9675

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delfiterradas merged 6 commits into from
Jan 20, 2026
Merged

Fix abundance_differential_filter to only generate one normalized matrix with dream #9675

delfiterradas merged 6 commits into from
Jan 20, 2026

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@delfiterradas delfiterradas commented Jan 15, 2026

PR checklist

Closes nf-core/differentialabundance#616

  • 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 module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Broadcast software version numbers to topic: versions - See version_topics
  • Follow the naming conventions.
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  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
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      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
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@delfiterradas delfiterradas self-assigned this Jan 15, 2026
@delfiterradas delfiterradas marked this pull request as ready for review January 16, 2026 15:08
@delfiterradas delfiterradas marked this pull request as draft January 16, 2026 15:39
@delfiterradas delfiterradas marked this pull request as ready for review January 16, 2026 17:05
@delfiterradas delfiterradas requested a review from grst January 16, 2026 17:42
pinin4fjords
pinin4fjords reviewed Jan 19, 2026
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pinin4fjords
pinin4fjords requested changes Jan 19, 2026
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I'm assuming the ext.when thing is a relic?

@delfiterradas delfiterradas added this pull request to the merge queue Jan 20, 2026
Merged via the queue into nf-core:master with commit a4d65df Jan 20, 2026
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@delfiterradas delfiterradas deleted the dream_norm branch January 20, 2026 13:13
delfiterradas added a commit to delfiterradas/modules that referenced this pull request Jan 20, 2026
@delfiterradas
Fix abundance_differential_filter to only generate one normalized m…
6a6e919 
…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
github-merge-queue bot pushed a commit that referenced this pull request Jan 20, 2026
@delfiterradas @prototaxites
@takiifujita-ui @charles-plessy @jfy133 @SPPearce @vagkaratzas @maxulysse @Ales-ibt @Krannich479
Emit both png and pdf plots in deseq2 (#9654)
7c9b5e9 
* Emit both png and pdf plots

* Update stub test

* Update `meta.yml`

* Remove trailing whitespace

* Correct meta.yml

* fix(mitohifi): Update mitohifi to topic versions, add log, and tweak module operation (#9698)

fix(mitohifi): update mitohifi to version topics, add a log file output, and change input processing to allow multiple input files

* Samtools update nf35 (#9699)

* 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 <[email protected]>
Co-authored-by: Charles Plessy <[email protected]>

* Update CHECKM2_PREDICT to allow more flexible pickup of database file (#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 <[email protected]>

* 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 <[email protected]>

* strict syntax + versions topic (#9693)

* strict syntax + versions topic

* simplified eval for versions and added ontologies

* snpeff and vep -  multiqc_files topics (#9677)

* snapshots

* fix meta + snapshots

* reports-> multiqc_files

* add task.process

* fix snapshots

* Update/local cd search (#9696)

* Update container image URL for localcdsearch

* Update container URL for localcdsearch module

* Samtools quickcheck (#9678)

* 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

* Fix `abundance_differential_filter` to only generate one normalized matrix with `dream` (#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

* Update png output

---------

Co-authored-by: Jim Downie <[email protected]>
Co-authored-by: takiifujita-ui <[email protected]>
Co-authored-by: Takii-Fujita <[email protected]>
Co-authored-by: Charles Plessy <[email protected]>
Co-authored-by: James A. Fellows Yates <[email protected]>
Co-authored-by: Simon Pearce <[email protected]>
Co-authored-by: Evangelos Karatzas <[email protected]>
Co-authored-by: Maxime U Garcia <[email protected]>
Co-authored-by: Alejandra Escobar <[email protected]>
Co-authored-by: Thomas Krannich <[email protected]>
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@pinin4fjords pinin4fjords pinin4fjords approved these changes

@grst grst grst approved these changes

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Dream normalized matrix should be generated only once

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