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Benchmarking #118

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Benchmarking #118

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Commits on Jul 18, 2024

  1. Replicate circRNA discovery for benchmarking

    @nictru @Fabian-Boehm
    nictru authored and Fabian-Boehm committed Jul 18, 2024
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  2. Implement Jaccard calculation

    @nictru @Fabian-Boehm
    nictru authored and Fabian-Boehm committed Jul 18, 2024
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  3. Implement jaccard file collection

    @nictru @Fabian-Boehm
    nictru authored and Fabian-Boehm committed Jul 18, 2024
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  4. Add benchmarking multiqc configuration

    @nictru @Fabian-Boehm
    nictru authored and Fabian-Boehm committed Jul 18, 2024
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  5. Group benchmark multiqc sections

    @nictru @Fabian-Boehm
    nictru authored and Fabian-Boehm committed Jul 18, 2024
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  6. implemented location mapping

    @Fabian-Boehm
    Fabian Boehm authored and Fabian-Boehm committed Jul 18, 2024
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  7. diagnostics: ch_joined not found, added files

    @Fabian-Boehm
    Fabian Böhm authored and Fabian-Boehm committed Jul 18, 2024
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  8. Added Overlap location plots

    @Fabian-Boehm
    Fabian Böhm authored and Fabian-Boehm committed Jul 18, 2024
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  9. prepare seq_depth data, trimgalore reports in benchmarking.nf

    @Fabian-Boehm
    Fabian Böhm authored and Fabian-Boehm committed Jul 18, 2024
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  10. sequencing depth pearson correllation computation

    @Fabian-Boehm
    Fabian Böhm authored and Fabian-Boehm committed Jul 18, 2024
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  11. config files added to git

    @Fabian-Boehm
    Fabian Böhm authored and Fabian-Boehm committed Jul 18, 2024
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  12. Postmerge fixes

    @Fabian-Boehm
    Fabian-Boehm committed Jul 18, 2024
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  13. diagnostic: comparison to older version needed

    @Fabian-Boehm
    Fabian-Boehm committed Jul 18, 2024
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  14. Fixed benchmarking.nf input to be tool specific as previously. Fixed … 

    …Pearson-correllation. Implemented collection of correlation values.
    @Fabian-Boehm
    Fabian-Boehm committed Jul 18, 2024
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  15. added sequence depth to mulitiqc. Changed labels and layout of locati… 

    …on plots
    @Fabian-Boehm
    Fabian-Boehm committed Jul 18, 2024
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  16. pre-commit run pass. Deleted redundant module

    @Fabian-Boehm
    Fabian-Boehm committed Jul 18, 2024
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  17. Added sections to multiqc, fixed an issue where the Seq-depth-correla… 

    …tion was calculated from the wrong files
    @Fabian-Boehm
    Fabian-Boehm committed Jul 18, 2024
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  18. Fixed an issue, where the Strands in the multiqc locationplots would … 

    …sometimes apear the wrong way round
    @Fabian-Boehm
    Fabian-Boehm committed Jul 18, 2024
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  19. cosmetic cleanup of the benchmarking module.

    @Fabian-Boehm
    Fabian-Boehm committed Jul 18, 2024
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  20. Fixed an issue where CIRCRNA_DISCOVERY_BENCHMARKING did not get all n… 

    …ecessary inputs after the merge
    @Fabian-Boehm
    Fabian-Boehm committed Jul 18, 2024
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  21. readded missing module configs after rebase

    @Fabian-Boehm
    Fabian-Boehm committed Jul 18, 2024
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Commits on Aug 1, 2024

  1. Ensured correct syntax, removed unnecessary specifications

    @Fabian-Boehm
    Fabian-Boehm committed Aug 1, 2024
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  2. Merge branch 'dev' into benchmarking after find_circ fix

    @Fabian-Boehm
    Fabian-Boehm committed Aug 1, 2024
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  3. removed debugging statements

    @Fabian-Boehm
    Fabian-Boehm committed Aug 1, 2024
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Commits on Aug 19, 2024

  1. added version control as per requested changes (15.07.24) and GENOMECOV

    @Fabian-Boehm
    Fabian-Boehm committed Aug 19, 2024
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Commits on Sep 5, 2024

  1. Merge remote-tracking branch 'origin/dev' into benchmarking

    @nictru
    nictru committed Sep 5, 2024
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  2. Minor adjustments for compatibility

    @nictru
    nictru committed Sep 5, 2024
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  3. Remove outdated module configs

    @nictru
    nictru committed Sep 5, 2024
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  4. Remove some unnecessary imports

    @nictru
    nictru committed Sep 5, 2024
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Commits on Sep 13, 2024

  1. implemented requested changes from 5.9.24

    @Fabian-Boehm
    Fabian-Boehm committed Sep 13, 2024
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Commits on Sep 16, 2024

  1. fixed some issues that pervented termination

    @Fabian-Boehm
    Fabian-Boehm committed Sep 16, 2024
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