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Update print format of BBMAP/repair.sh version #7332

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Update print format of BBMAP/repair.sh version #7332

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Update of the print format of the tool version

PR checklist

Closes #7331

  • [ X ] This comment contains a description of changes (with reason).
  • [ X ] If you've fixed a bug or added code that should be tested, add tests!
  • [ X ] If necessary, include test data in your PR.
  • [ X ] Remove all TODO statements.
  • [ X ] Emit the versions.yml file.
  • [ X ] Follow the naming conventions.
  • [ X ] Follow the parameters requirements.
  • [ X ] Follow the input/output options guidelines.
  • [ X ] Add a resource label
  • [ X ] 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:
      • [ X ] nf-core modules test <MODULE> --profile docker
      • [ X ] nf-core modules test <MODULE> --profile singularity
      • [ X ] nf-core modules test <MODULE> --profile conda

mazzalab and others added 17 commits January 13, 2025 19:51
@mazzalab
Refactor fastq and report variable names for consistency across wiper…
c7c71d3 
…tools modules
@mazzalab
Refactor variable names for consistency in fastq and report processin…
9ec69f2 
…g modules
@mazzalab
Update test assertions to reflect changes in output variable names in…
a5dd7d4 
… fastqwiper module
@mazzalab
Update test assertions to match changes in report output structure in…
fcf17e6 
… fastqwiper tests
@Jorisvansteenbrugge @SPPearce @mazzalab
pypgx/runngspipeline (nf-core#6823)
1da34ed 
* pypgx/runngspipeline

* update PR comments

---------

Co-authored-by: Jorisvansteenbrugge <7196110+Jorisvansteenbrugge@users.noreply.github.com>
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
@renovate @mazzalab
Update actions/upload-artifact digest to 65c4c4a (nf-core#7293)
ca15288 
Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
@vagkaratzas @mazzalab
fixed typo that produces "unknown recognition error type: groovyjarja… (
3b4b6d0 
nf-core#7295)

fixed typo that produces "unknown recognition error type: groovyjarjarantlr4.v4.runtime.LexerNoViableAltException" in pipelines
@prototaxites @mazzalab
Update Galah & add nf-tests (nf-core#7291)
a07564d 
* Update Galah & add nf-tests

* Fix linting

* Update main.nf

* Update inputs in meta.yml

* Fix missing snapshot output from broken test
@nschcolnicov @SPPearce @mazzalab
Added nftests to gseagsea (nf-core#7266)
e02aebd 
* Added nftests to gseagsea

* Update input files

* fix nftests

* Address PR comments

* Add seed setting parameter for stabilizing results

* Fix linting

* Add default random seed

* Update datasets paths

---------

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
@GallVp @mazzalab
Bumped lima to 2.12.0 (nf-core#7294)
62afa8f
@mazzalab
Update container version to 1.1.4 and modify test names for clarity
2b86a96
@mazzalab
Merge branch 'master' into master
d19a459
@mazzalab
Remove obsolete test cases from fastqscatter and clean up pytest modu…
c3f5a4f 
…le configuration
@mazzalab
Update wipertools version to 1.1.4 in environment.yml files for fastq…
897f693 
…gather, fastqscatter, fastqwiper, and reportgather
@mazzalab
Update timestamps in fastqscatter test snapshots for consistency
e970c84
@mazzalab
Merge branch 'nf-core:master' into master
aab699f
@mazzalab
Update BBMAP_REPAIR process to use bbversion.sh for version retrieval
7509955
@mazzalab mazzalab self-assigned this Jan 18, 2025
@mazzalab mazzalab enabled auto-merge January 19, 2025 08:05
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update module: BBMAP/REPAIR.SH
6 participants
@mazzalab @Jorisvansteenbrugge @vagkaratzas @prototaxites @nschcolnicov @GallVp