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Shigapass #6636

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Shigapass #6636

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Commits on Oct 30, 2024

  1. add shigapass module

    @maxlcummins
    maxlcummins committed Oct 30, 2024
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  2. remove unnecessary bk file

    @maxlcummins
    maxlcummins committed Oct 30, 2024
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  3. fixed some linter flagged issues

    @maxlcummins
    maxlcummins committed Oct 30, 2024
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  4. updates for testing

    @maxlcummins
    maxlcummins committed Oct 30, 2024
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  5. remove name field

    @maxlcummins
    maxlcummins committed Oct 30, 2024
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  6. remove error detailing tool url

    @maxlcummins
    maxlcummins committed Oct 30, 2024
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  7. add main.nf.test.snap and update main.nf.test as per pull request nf-… 

    …core#6636
    @maxlcummins
    maxlcummins committed Oct 30, 2024
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  8. change readlink -f to ls as per PR feedback

    @maxlcummins
    maxlcummins committed Oct 30, 2024
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  9. add gzip support via rpetit3 and fix lint errors

    @maxlcummins
    maxlcummins authored and maxlcummins committed Oct 30, 2024
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  10. fix error in args definition

    @maxlcummins
    maxlcummins committed Oct 30, 2024
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  11. change shigapass main.nf to pass nf-core tests

    @maxlcummins
    maxlcummins committed Oct 30, 2024
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  12. Update meta.yml 

    fix meta flag re linting/testing errors: "is not of type 'array'."
    @maxlcummins
    maxlcummins committed Oct 30, 2024
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  13. Update main.nf 

    Fix typo in singularity container
    @maxlcummins
    maxlcummins committed Oct 30, 2024
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  14. Add variable output tolerance for shigapass 

    Shigella flexneri genomes will result in an extra output - fixed the module to handle this
    @maxlcummins
    maxlcummins authored Oct 30, 2024
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Commits on Oct 31, 2024

  1. Update Shigapass main.nf 

    Change shigapass module output delimiter to tab from semicolon
    @maxlcummins
    maxlcummins authored Oct 31, 2024
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  2. Merge branch 'nf-core:master' into shigapass

    @maxlcummins
    maxlcummins authored Oct 31, 2024
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