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fixed typo that produces "unknown recognition error type: groovyjarja… #7295

Merged
merged 2 commits into from
Jan 13, 2025
Merged

fixed typo that produces "unknown recognition error type: groovyjarja… #7295

merged 2 commits into from
Jan 13, 2025

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vagkaratzas
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…rantlr4.v4.runtime.LexerNoViableAltException" in pipelines

PR checklist

Closes #XXX

  • 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 vagkaratzas added this pull request to the merge queue Jan 13, 2025
Merged via the queue into master with commit c70357e Jan 13, 2025
27 checks passed
@vagkaratzas vagkaratzas deleted the pigz-uncompress branch January 13, 2025 08:56
mazzalab pushed a commit to mazzalab/nf-core_modules that referenced this pull request Jan 18, 2025
@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
github-merge-queue bot pushed a commit that referenced this pull request Jan 18, 2025
@mazzalab @Jorisvansteenbrugge
@SPPearce @renovate @vagkaratzas @prototaxites @nschcolnicov @GallVp
Bump wipertools to 1.1.4 (#7328)
e7f7c0f 
* Refactor fastq and report variable names for consistency across wipertools modules

* Refactor variable names for consistency in fastq and report processing modules

* Update test assertions to reflect changes in output variable names in fastqwiper module

* Update test assertions to match changes in report output structure in fastqwiper tests

* pypgx/runngspipeline (#6823)

* 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>

* Update actions/upload-artifact digest to 65c4c4a (#7293)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

* fixed typo that produces "unknown recognition error type: groovyjarja… (#7295)

fixed typo that produces "unknown recognition error type: groovyjarjarantlr4.v4.runtime.LexerNoViableAltException" in pipelines

* Update Galah & add nf-tests (#7291)

* Update Galah & add nf-tests

* Fix linting

* Update main.nf

* Update inputs in meta.yml

* Fix missing snapshot output from broken test

* Added nftests to gseagsea (#7266)

* 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>

* Bumped lima to 2.12.0 (#7294)

* Update container version to 1.1.4 and modify test names for clarity

* Remove obsolete test cases from fastqscatter and clean up pytest module configuration

* Update wipertools version to 1.1.4 in environment.yml files for fastqgather, fastqscatter, fastqwiper, and reportgather

* Update timestamps in fastqscatter test snapshots for consistency

---------

Co-authored-by: Joris van Steenbrugge <Jorisvansteenbrugge@users.noreply.github.com>
Co-authored-by: Jorisvansteenbrugge <7196110+Jorisvansteenbrugge@users.noreply.github.com>
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>
Co-authored-by: Jim Downie <19718667+prototaxites@users.noreply.github.com>
Co-authored-by: Nicolás Schcolnicov <90359308+nschcolnicov@users.noreply.github.com>
Co-authored-by: Usman Rashid <usman@smme.edu.pk>
github-merge-queue bot pushed a commit that referenced this pull request Jan 22, 2025
@mazzalab @Jorisvansteenbrugge
@SPPearce @renovate @vagkaratzas @prototaxites @nschcolnicov @GallVp
Update print format of BBMAP/repair.sh version (#7332)
4c81a35 
* Refactor fastq and report variable names for consistency across wipertools modules

* Refactor variable names for consistency in fastq and report processing modules

* Update test assertions to reflect changes in output variable names in fastqwiper module

* Update test assertions to match changes in report output structure in fastqwiper tests

* pypgx/runngspipeline (#6823)

* 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>

* Update actions/upload-artifact digest to 65c4c4a (#7293)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

* fixed typo that produces "unknown recognition error type: groovyjarja… (#7295)

fixed typo that produces "unknown recognition error type: groovyjarjarantlr4.v4.runtime.LexerNoViableAltException" in pipelines

* Update Galah & add nf-tests (#7291)

* Update Galah & add nf-tests

* Fix linting

* Update main.nf

* Update inputs in meta.yml

* Fix missing snapshot output from broken test

* Added nftests to gseagsea (#7266)

* 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>

* Bumped lima to 2.12.0 (#7294)

* Update container version to 1.1.4 and modify test names for clarity

* Remove obsolete test cases from fastqscatter and clean up pytest module configuration

* Update wipertools version to 1.1.4 in environment.yml files for fastqgather, fastqscatter, fastqwiper, and reportgather

* Update timestamps in fastqscatter test snapshots for consistency

* Update BBMAP_REPAIR process to use bbversion.sh for version retrieval

* Update test snapshots with new version hashes and timestamps

---------

Co-authored-by: Joris van Steenbrugge <Jorisvansteenbrugge@users.noreply.github.com>
Co-authored-by: Jorisvansteenbrugge <7196110+Jorisvansteenbrugge@users.noreply.github.com>
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>
Co-authored-by: Jim Downie <19718667+prototaxites@users.noreply.github.com>
Co-authored-by: Nicolás Schcolnicov <90359308+nschcolnicov@users.noreply.github.com>
Co-authored-by: Usman Rashid <usman@smme.edu.pk>
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@mashehu mashehu mashehu approved these changes

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@vagkaratzas @mashehu