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add module mat2json#10340

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CaroAMN merged 16 commits intonf-core:masterfrom
CaroAMN:mat2json
Mar 11, 2026
Merged

add module mat2json#10340
CaroAMN merged 16 commits intonf-core:masterfrom
CaroAMN:mat2json

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@CaroAMN CaroAMN commented Mar 5, 2026

PR checklist

Closes #10339

  • 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

Conda is not an option

@CaroAMN CaroAMN self-assigned this Mar 5, 2026
@CaroAMN CaroAMN requested a review from mashehu March 5, 2026 19:31
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CaroAMN commented Mar 5, 2026

lint error i think is because i use ADD and not COPY. I can't use COPY in my docker file because i download the binary application from a git repository.

And i have no conda package, and i don't know how to prevent the conda test from running

@CaroAMN CaroAMN requested review from a team as code owners March 6, 2026 09:41
CaroAMN and others added 4 commits March 11, 2026 10:07
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
@CaroAMN CaroAMN added this pull request to the merge queue Mar 11, 2026
Merged via the queue into nf-core:master with commit 7a7f64a Mar 11, 2026
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@CaroAMN CaroAMN deleted the mat2json branch March 11, 2026 10:18
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new module: mat2json

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