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Add new module: disambiguate#10917

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ctuni wants to merge 18 commits intonf-core:masterfrom
ctuni:disambiguate
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Add new module: disambiguate#10917
ctuni wants to merge 18 commits intonf-core:masterfrom
ctuni:disambiguate

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@ctuni ctuni commented Mar 16, 2026 •
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This pull request introduces a new disambiguate module for, which enables the disambiguation of sequencing reads aligned to two different organisms (e.g., human and mouse).

PR checklist

Closes #10915

  • 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.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • 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
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

srisarya
srisarya reviewed Mar 17, 2026
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mostly looks good to me, but maybe get a more senior person too

gmarenne and others added 16 commits March 17, 2026 12:23
@gmarenne @LouisLeNezet @ctuni
topic migration crispresso2 (nf-core#10827)
a4f0798 
* topic migration crispresso2

* topic migration crispresso2

* topic migration crispresso2

* topic migration crispresso2

* topic migration crispresso2

---------

Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com>
@atrigila @ctuni
add missing channels for workflow outputs (nf-core#10918)
92b5ffd 
* add missing channels for workflow outputs

* collect bcl2fastq undetermined
@srisarya @ctuni
Hisat build springcleaning (nf-core#10686)
1af66d2 
* remove redundancy in mem opts for hisat2/build
- remove conflicting 'process_high_memory' label
- fix error on missing memory instead of defaulting to MAX_VALUE (remove redundant line 37, fold loud fail into script)

* re-test module, passing

* update hisat2 version, match container from seqera containers, remove unneeded samtools dependency

* change versions in hisat2 align too

* return singularity

* add name as co author

* add singularity docker 2 ways (build: just hisat2-2.2.2, align: hisat2-2.2.2 + samtools-1.23)

* update snap

* update snap
@LiaOb21 @camlloyd
@FernandoDuarteF @ctuni
Abyss (nf-core#10647)
3806bda 
* working on abyss module

* abyss ready

* fix linting

* Update description for abyss_abysspe

* Removing TODOs

Co-authored-by: Cameron Lloyd <lloyd@med.unideb.hu>

* Removing TODOs

Co-authored-by: Cameron Lloyd <lloyd@med.unideb.hu>

* output is now gzipped

* Update modules/nf-core/abyss/abysspe/main.nf

Co-authored-by: Fernando Duarte <123090819+FernandoDuarteF@users.noreply.github.com>

* Update modules/nf-core/abyss/abysspe/tests/main.nf.test

Co-authored-by: Cameron Lloyd <lloyd@med.unideb.hu>

* updating abyss tests

* Update modules/nf-core/abyss/abysspe/meta.yml

Co-authored-by: Cameron Lloyd <lloyd@med.unideb.hu>

* Clarify ontology references in meta.yml

Added comments to ontology references for clarity.

---------

Co-authored-by: Cameron Lloyd <lloyd@med.unideb.hu>
Co-authored-by: Fernando Duarte <123090819+FernandoDuarteF@users.noreply.github.com>
@EfraMP @ctuni
Migrate gfaffix version topics (nf-core#10905)
ca8234d 
* Migrate gfaffix version topics

* Fix linting

* fix typo

* Fix reviews
@tgelafr-pfzr @ctuni
stageAs FASTQC input files to avoid basename file collisions (nf-core…
9015d4b 
…#10924)
@camlloyd @mashehu @ctuni
update module: duphold (nf-core#10822)
10f88b8 
* Update main.nf

* Update meta.yml

* Update main.nf.test

* Update snaps

* Add bio.tools ID

* Update modules/nf-core/duphold/main.nf

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

* Update meta.yml

* Fix version

* Update meta.yml

* Update meta.yml

---------

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
@Kevin-Brockers @mashehu @ctuni
updated macs3 to 3.0.4 and added topic channel (nf-core#10926)
23a8f0f 
* Updated macs3 to 3.0.4 and added topics channel

* updated meta

* Updated meta - contributor & topcis eval

* fix formatting

* fixed formatting with pre-commit hook

* Update modules/nf-core/macs3/callpeak/main.nf

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

* fixed meta

---------

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
@lucaspatel @ctuni
Add ViralConsensus module (nf-core#9655)
9da7349 
* feat: Added ViralConsensus module

* fix: update test snapshots for Docker compatibility

* fix: task.ext to optional inputs

* fix: update configuration of ext.args in tests

* fix: simplify test asserts, though breaks linting

* fix: add meta map to fasta input

* fix: tests match and sed/head handling

* chore: remove shell redirect
@prototaxites @ctuni
fix(purge_dups): re-add prefix to output file names (nf-core#10919)
d1d62d3 
fix(purge_dups): not using prefix?????????
@sofiademmou @SPPearce @ctuni
Add module for vcfexpress (nf-core#10409)
f71199b 
* added module for vcfexpress

* added suffix and fixed linting

* removed TODO and fixed formatting

* fixed testing

* Update modules/nf-core/vcfexpress/main.nf

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

* Update modules/nf-core/vcfexpress/tests/main.nf.test

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

* updated meta.yml

* added creation of lua file in test

* removed 'vcfexpress' from version number in topic

* fixed formatting

* Update modules/nf-core/vcfexpress/tests/main.nf.test

---------

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
@pinin4fjords @claude @ctuni
feat(tximeta/tximport): add tag directive (nf-core#10927)
b0910f0 
feat(tximeta/tximport): add tag directive for process labeling

Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
@ieduba @ctuni
Add new module: saltshaker/classify (nf-core#10914)
47f72f7 
* add saltshaker classify module and tests

* pin pip version

* add saltshaker classify module and tests

* pin pip version

* update test with nf-core saltshaker/call

* fix linting

* add saltshaker classify module and tests

* pin pip version

* update test with nf-core saltshaker/call

* fix linting

* edits from review

* update snaps and meta.yml

* only make vcf in stub if vcf is in args

* add no-vcf tests

---------

Co-authored-by: Irene Duba <irene.duba@scilifelab.se>
@pinin4fjords @claude @ctuni
feat: add topic version emission to quant-related modules (nf-core#10931
8af92b6 
)

Convert custom/tx2gene, tximeta/tximport, and
summarizedexperiment/summarizedexperiment to emit versions via
topic channels, enabling automatic version collection in
downstream subworkflows.

Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
@ctuni
removed redundant assertions
8cd6ee6
@ctuni
Merge branch 'master' into disambiguate
4671631
@srisarya srisarya enabled auto-merge March 17, 2026 11:32
@srisarya
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srisarya commented Mar 17, 2026

PR closed since auto merge will happen :)

@srisarya srisarya closed this Mar 17, 2026
auto-merge was automatically disabled March 17, 2026 11:33

Pull request was closed

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new module: disambiguate