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Minia update#11065

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LiaOb21 wants to merge 12 commits intonf-core:masterfrom
LiaOb21:minia_update
Open

Minia update#11065
LiaOb21 wants to merge 12 commits intonf-core:masterfrom
LiaOb21:minia_update

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@LiaOb21
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@LiaOb21 LiaOb21 commented Mar 27, 2026

This PR contains an update for Minia.
Changes include:

  • fasta files are now outputted as gzipped
  • the module outputs the log file
  • migration to topic channels

PR checklist

Closes #11056

  • 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

@LiaOb21
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LiaOb21 commented Mar 27, 2026

@nf-core-bot fix linting please

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LiaOb21 commented Mar 27, 2026

Sorry, I think I did another mistake

LiaOb21 and others added 4 commits March 27, 2026 15:57
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
file(process.out.h5[0][1]).name,
process.out.versions,
file(process.out.log[0][1]).name,
process.out.versions_minia,
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Suggested change
process.out.versions_minia,
process.out.findAll { key, val -> key.startsWith('versions') },

- minia:
type: string
description: The name of the tool
- minia -v | grep Minia | sed 's/Minia version //g':
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Suggested change
- minia -v | grep Minia | sed 's/Minia version //g':
- minia -v | sed -n 's/Minia version //p':

- minia:
type: string
description: The name of the tool
- minia -v | grep Minia | sed 's/Minia version //g':
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Suggested change
- minia -v | grep Minia | sed 's/Minia version //g':
- minia -v | sed -n 's/Minia version //p':

@@ -4,17 +4,18 @@ process MINIA {

conda "${moduleDir}/environment.yml"
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can you update the version number in this file as well please

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update module: minia

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