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Merged
vagkaratzas merged 16 commits into from
Dec 15, 2025
Merged

Update trimgalore #9570

vagkaratzas merged 16 commits into from
Dec 15, 2025

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@vagkaratzas
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@vagkaratzas vagkaratzas commented Dec 15, 2025 •
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Updated to latest container and new output syntax. nf-tests and meta.yml file also updated.

PR checklist

  • 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.
  • Emit the versions.yml file.
  • 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

vagkaratzas and others added 12 commits December 12, 2025 14:11
@vagkaratzas
testing solo trim-galore container, without adding extra cutadapt and…
1c8c358 
… pigz
@nvnieuwk @vagkaratzas
Syntax updates and topic version for manta modules (#9556)
0f8c767 
* update manta germline

* topics convertinversion

* topics convertinversion

* topics manta/somatic

* topics manta/tumoronly
@nvnieuwk @vagkaratzas
Syntax updates and topics of jasminesv (#9554)
80c23a0 
syntax updates and topics of jasminesv
@jkh00 @nf-core-bot @vagkaratzas
Update Modkit pileup (#9553)
bccaf52 
* update yaml

* update main.nf

* modified test runs

* update bedmethyltobigwig tests

* update main

* update snapshot

* fix linting

* update snapshots

* remove config

* update module_args

* [automated] Fix linting with Prettier

* changed name

* update main

---------

Co-authored-by: ra25wog <jin.khoo@campus.lmu.de>
Co-authored-by: nf-core-bot <core@nf-co.re>
@LouisLeNezet @vagkaratzas
Standarize and alignment for all imputation and alignment modules (#9566
140c2c5 
)

* Standarize and alignment

* Fix glimpse2 sbwf test

* Fix test

* Add comment

* Update snapshot

---------

Co-authored-by: LouisLeNezet <louislenezet@gmaio.com>
@renovate @vagkaratzas
Update Infrastructural dependencies
2baa9f1
@LouisLeNezet @vagkaratzas
Remove .view() (#9567)
e1abd32
@fellen31 @vagkaratzas
Bump strdrop to 0.3.1 (#9565)
9c5de94
@LouisLeNezet @vagkaratzas
Remove unecessary tags (#9568)
0afa0ce 
* Remove .view()

* Remove unecessary tags
@vagkaratzas
latest container, with cutadapt 5.2
e2a164d
@vagkaratzas
new output syntax, nf-tests updated, meta updated
8e4b6ea
@vagkaratzas
meta yml lint fixed
fbcb6c7
@vagkaratzas vagkaratzas requested review from a team as code owners December 15, 2025 15:06
FelixKrueger
FelixKrueger approved these changes Dec 15, 2025
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The changes appear sensible to me. Version syntax is undergoing updating - and this change removes dependency on outdated tools such as Cutadapt 4.9 or pigz 2.8.

Thanks!

@vagkaratzas vagkaratzas added this pull request to the merge queue Dec 15, 2025
Merged via the queue into master with commit 1b32b48 Dec 15, 2025
71 checks passed
@vagkaratzas vagkaratzas deleted the update-trimgalore branch December 15, 2025 16:07
vagkaratzas added a commit that referenced this pull request Dec 15, 2025
@vagkaratzas @nvnieuwk
@jkh00 @nf-core-bot @LouisLeNezet @renovate @fellen31
Update trimgalore (#9570)
6546c99 
* testing solo trim-galore container, without adding extra cutadapt and pigz

* Syntax updates and topic version for manta modules (#9556)

* update manta germline

* topics convertinversion

* topics convertinversion

* topics manta/somatic

* topics manta/tumoronly

* Syntax updates and topics of jasminesv (#9554)

syntax updates and topics of jasminesv

* Update `Modkit pileup`  (#9553)

* update yaml

* update main.nf

* modified test runs

* update bedmethyltobigwig tests

* update main

* update snapshot

* fix linting

* update snapshots

* remove config

* update module_args

* [automated] Fix linting with Prettier

* changed name

* update main

---------

Co-authored-by: ra25wog <jin.khoo@campus.lmu.de>
Co-authored-by: nf-core-bot <core@nf-co.re>

* Standarize and alignment for all imputation and alignment modules (#9566)

* Standarize and alignment

* Fix glimpse2 sbwf test

* Fix test

* Add comment

* Update snapshot

---------

Co-authored-by: LouisLeNezet <louislenezet@gmaio.com>

* Update Infrastructural dependencies

* Remove .view() (#9567)

* Bump strdrop to 0.3.1 (#9565)

* Remove unecessary tags (#9568)

* Remove .view()

* Remove unecessary tags

* latest container, with cutadapt 5.2

* new output syntax, nf-tests updated, meta updated

* meta yml lint fixed

* trying to fix lint

* lint fix with nf-core tools 3.6.0dev

* removing TRIMGALORE versions output from the FASTQ_FASTQC_UMITOOLS_TRIMGALORE subworkflow

---------

Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
Co-authored-by: Jinn <155078830+jkh00@users.noreply.github.com>
Co-authored-by: ra25wog <jin.khoo@campus.lmu.de>
Co-authored-by: nf-core-bot <core@nf-co.re>
Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com>
Co-authored-by: LouisLeNezet <louislenezet@gmaio.com>
Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com>
georgiakes pushed a commit to georgiakes/modules that referenced this pull request Dec 30, 2025
@vagkaratzas @nvnieuwk
@jkh00 @nf-core-bot @LouisLeNezet @renovate @fellen31 @georgiakes
Update trimgalore (nf-core#9570)
a0f2888 
* testing solo trim-galore container, without adding extra cutadapt and pigz

* Syntax updates and topic version for manta modules (nf-core#9556)

* update manta germline

* topics convertinversion

* topics convertinversion

* topics manta/somatic

* topics manta/tumoronly

* Syntax updates and topics of jasminesv (nf-core#9554)

syntax updates and topics of jasminesv

* Update `Modkit pileup`  (nf-core#9553)

* update yaml

* update main.nf

* modified test runs

* update bedmethyltobigwig tests

* update main

* update snapshot

* fix linting

* update snapshots

* remove config

* update module_args

* [automated] Fix linting with Prettier

* changed name

* update main

---------

Co-authored-by: ra25wog <jin.khoo@campus.lmu.de>
Co-authored-by: nf-core-bot <core@nf-co.re>

* Standarize and alignment for all imputation and alignment modules (nf-core#9566)

* Standarize and alignment

* Fix glimpse2 sbwf test

* Fix test

* Add comment

* Update snapshot

---------

Co-authored-by: LouisLeNezet <louislenezet@gmaio.com>

* Update Infrastructural dependencies

* Remove .view() (nf-core#9567)

* Bump strdrop to 0.3.1 (nf-core#9565)

* Remove unecessary tags (nf-core#9568)

* Remove .view()

* Remove unecessary tags

* latest container, with cutadapt 5.2

* new output syntax, nf-tests updated, meta updated

* meta yml lint fixed

* trying to fix lint

* lint fix with nf-core tools 3.6.0dev

* removing TRIMGALORE versions output from the FASTQ_FASTQC_UMITOOLS_TRIMGALORE subworkflow

---------

Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
Co-authored-by: Jinn <155078830+jkh00@users.noreply.github.com>
Co-authored-by: ra25wog <jin.khoo@campus.lmu.de>
Co-authored-by: nf-core-bot <core@nf-co.re>
Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com>
Co-authored-by: LouisLeNezet <louislenezet@gmaio.com>
Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com>
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7 participants

@vagkaratzas @FelixKrueger @nvnieuwk @jkh00 @LouisLeNezet @fellen31