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Implement ciriquant quantification #172

Merged
merged 49 commits into from
Sep 26, 2024
Merged

Implement ciriquant quantification #172

merged 49 commits into from
Sep 26, 2024

Commits on Aug 23, 2024

  1. Simplify ciriquant config creation

    @nictru
    nictru committed Aug 23, 2024
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  2. Implement support for single-stranded libraries

    @nictru
    nictru committed Aug 23, 2024
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  3. Add support for bed files in ciriquant

    @nictru
    nictru committed Aug 23, 2024
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  4. Add support for multiple quantification methods

    @nictru
    nictru committed Aug 23, 2024
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  5. Implement first bit of global ciriquant quantification

    @nictru
    nictru committed Aug 23, 2024
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  6. Enable ciriquant gene quantification

    @nictru
    nictru committed Aug 23, 2024
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Commits on Aug 24, 2024

  1. Implement ciriquant circ count extraction

    @nictru
    nictru committed Aug 24, 2024
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  2. Generalize gffread module

    @nictru
    nictru committed Aug 24, 2024
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  3. Further generalize gffread

    @nictru
    nictru committed Aug 24, 2024
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  4. Improve gffread fasta creation

    @nictru
    nictru committed Aug 24, 2024
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  5. Use nf-core gffread module and add pygtftk

    @nictru
    nictru committed Aug 24, 2024
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  6. Implement gene expression extraction

    @nictru
    nictru committed Aug 24, 2024
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  7. Implement ciriquant expression column naming

    @nictru
    nictru committed Aug 24, 2024
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  8. Implement ciriquant expression joining

    @nictru
    nictru committed Aug 24, 2024
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  9. Improve ciriquant handling

    @nictru
    nictru committed Aug 24, 2024
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  10. Implement channel handling for ciriquant DEA

    @nictru
    nictru committed Aug 24, 2024
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  11. Implement ciriquant_dea samplesheet creation

    @nictru
    nictru committed Aug 24, 2024
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  12. Implement ciriquant DEA preprocessing

    @nictru
    nictru committed Aug 24, 2024
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  13. Implement capturing of stringtie results from ciriquant

    @nictru
    nictru committed Aug 24, 2024
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  14. Implement basic stringtie_prepde

    @nictru
    nictru committed Aug 24, 2024
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  15. Switch back to official ciriquant image to prevent stringtie compatib… 

    …ility problems
    @nictru
    nictru committed Aug 24, 2024
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  16. Rename ciriquant DE preparation module

    @nictru
    nictru committed Aug 24, 2024
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  17. Implement ciriquant de analysis

    @nictru
    nictru committed Aug 24, 2024
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  18. Improve ciriquant de output structure

    @nictru
    nictru committed Aug 24, 2024
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  19. Add ciriquant dockerfile

    @nictru
    nictru committed Aug 24, 2024
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  20. Update ciriquant docker image

    @nictru
    nictru committed Aug 24, 2024
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  21. Change ciriquant de output format to csv

    @nictru
    nictru committed Aug 24, 2024
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  22. Fix ciriquant de caching problems

    @nictru
    nictru committed Aug 24, 2024
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  23. Fix ciriquant de version capture problems

    @nictru
    nictru committed Aug 24, 2024
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  24. Make sure ciriquant de is only executed once per pairing

    @nictru
    nictru committed Aug 24, 2024
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  25. Add proper handling of ciriquant RDS

    @nictru
    nictru committed Aug 24, 2024
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Commits on Aug 25, 2024

  1. Update ciriquant image

    @nictru
    nictru committed Aug 25, 2024
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Commits on Aug 26, 2024

  1. Add retries to some memory intensive processes

    @nictru
    nictru committed Aug 26, 2024
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  2. Increase annotation resource label

    @nictru
    nictru committed Aug 26, 2024
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  3. Update ciriquant image

    @nictru
    nictru committed Aug 26, 2024
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Commits on Aug 27, 2024

  1. Improve ciriquant output directory definition

    @nictru
    nictru committed Aug 27, 2024
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  2. Tweak ciriquant publishdir definitions

    @nictru
    nictru committed Aug 27, 2024
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  3. Switch miRNA majority vote to polars

    @nictru
    nictru committed Aug 27, 2024
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  4. Fix some problems with updated mirna majority vote

    @nictru
    nictru committed Aug 27, 2024
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  5. Further improve mirna majority vote performance

    @nictru
    nictru committed Aug 27, 2024
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  6. Implement custom sample joining script

    @nictru
    nictru committed Aug 27, 2024
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  7. Fix minor bug in new sample joining module

    @nictru
    nictru committed Aug 27, 2024
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Commits on Sep 24, 2024

  1. Add default value for mature parameter

    @nictru
    nictru committed Sep 24, 2024
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  2. Fix null value in publishDir

    @nictru
    nictru committed Sep 24, 2024
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  3. Add quantification_tools to nextflow_schema.json

    @nictru
    nictru committed Sep 24, 2024
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Commits on Sep 25, 2024

  1. Fix editorconfig

    @nictru
    nictru committed Sep 25, 2024
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  2. Move save_intermediates to less prominent spot in docs

    @nictru
    nictru committed Sep 25, 2024
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  3. Simplify parameter docs structure

    @nictru
    nictru committed Sep 25, 2024
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  4. Fix schema error

    @nictru
    nictru committed Sep 25, 2024
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