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add dds/createproject#11094

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annaasklof wants to merge 13 commits intonf-core:masterfrom
annaasklof:dds/createProject
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add dds/createproject#11094
annaasklof wants to merge 13 commits intonf-core:masterfrom
annaasklof:dds/createProject

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@annaasklof annaasklof commented Mar 31, 2026

PR checklist

Closes #9003

  • 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

@annaasklof annaasklof added the new module Adding a new module label Mar 31, 2026
@mashehu
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mashehu commented Mar 31, 2026

@nf-core-bot fix linting

nf-core-bot and others added 12 commits March 31, 2026 13:15
@nf-core-bot
[automated] Fix linting with Prettier
2f6b78e
@camlloyd
new module: vcf2zarr/explode (nf-core#11092)
181acab 
* Add vcf2zarr/explode

* Restore comment
@vagkaratzas
Add caalm (nf-core#11087)
2153095 
* caalm init - seqera containers and env from pip

* main and meta init

* nf-test init

* switch to CAALM_CAALM and expect a second input of downloaded model

* switch to test-datasets file

* caalm_downloadmodels module

* nf-tests pass

* meta update and warning prevention during downloads

* export log, update tests to pass across platforms

* task.cpus added

* model levels split

* extra versions reported; python, torch, faiss

* downloadmodels output in tuple
@vagkaratzas
deprecate, switch cat/cat to find/concatenate (nf-core#11095)
88c3302 
* deprecate, switch cat/cat to find/concatenate

* replacing cat/cat in ltrretriever modules

* keeping one deprecation test only

* delete script and stub blocks

* pre-commit fix
@mahesh-panchal
Update GNU sort to comply to nf-core guidelines (nf-core#11072)
94e6aa4 
* Move ext.suffix to input

* Update tests to unify config

* Update test to use corrected input

* Add suffix to GNU SORT input
@renovate
Update pre-commit hook astral-sh/ruff-pre-commit to v0.15.8 (nf-core#…
cd77486 
…11100)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
@annaasklof
add dds/createproject
9bb0167
@annaasklof
align with nf-core/tools v 3.5.2
4652566
@annaasklof
align with nf-core/tools v 3.5.2
e978c7a
@annaasklof
remove previous files
1a193e8
@annaasklof
remove rest from bam
1a00158
@annaasklof
resolve conflicts
ca55a08
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new module: SciLifeLab DDS/createProject

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@annaasklof @mashehu @nf-core-bot @camlloyd @vagkaratzas @mahesh-panchal