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Update to DSL2 Best Practices #379

Merged
merged 53 commits into from
Jun 11, 2021
Merged

Update to DSL2 Best Practices #379

merged 53 commits into from
Jun 11, 2021

Commits on May 20, 2021

  1. feat: update main script and lib from DSL2 Best Practices

    @maxulysse
    maxulysse committed May 20, 2021
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  2. fix: add more file to lint ignore

    @maxulysse
    maxulysse committed May 20, 2021
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  3. feat: strip out unused functions

    @maxulysse
    maxulysse committed May 20, 2021
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  4. feat: update some modules

    @maxulysse
    maxulysse committed May 20, 2021
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  5. fix: HaplotypeCaller

    @maxulysse
    maxulysse committed May 20, 2021
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Commits on May 25, 2021

  1. feat: update msisensor

    @maxulysse
    maxulysse committed May 25, 2021
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  2. feat: update msisensor_msi

    @maxulysse
    maxulysse committed May 25, 2021
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  3. fix: Gstring.toString()

    @maxulysse
    maxulysse committed May 25, 2021
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  4. fix: output

    @maxulysse
    maxulysse committed May 25, 2021
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  5. remove unused file

    @maxulysse
    maxulysse committed May 25, 2021
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  6. remove white space

    @maxulysse
    maxulysse committed May 25, 2021
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  7. fix: output

    @maxulysse
    maxulysse committed May 25, 2021
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Commits on May 26, 2021

  1. fix: markduplicates subworkflow test

    @maxulysse
    maxulysse committed May 26, 2021
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  2. fix: subworkflow md finally fixed

    @maxulysse
    maxulysse committed May 26, 2021
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  3. fix: nextflow version

    @maxulysse
    maxulysse committed May 26, 2021
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Commits on May 27, 2021

  1. moving files and functions around

    @maxulysse
    maxulysse committed May 27, 2021
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Commits on May 28, 2021

  1. feat: update modules and move around functions, and possibly break ev… 

    …erything
    @maxulysse
    maxulysse committed May 28, 2021
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  2. fix: add .gitignore to .nf-core-lint.yml

    @maxulysse
    maxulysse committed May 28, 2021
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  3. fix: add new csv files

    @maxulysse
    maxulysse committed May 28, 2021
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  4. feat: simplify mapping script, update module, default test working

    @maxulysse
    maxulysse committed May 28, 2021
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  5. feat: cleanup files

    @maxulysse
    maxulysse committed May 28, 2021
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  6. cleanup

    @maxulysse
    maxulysse committed May 28, 2021
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  7. feat: simplify variant_calling

    @maxulysse
    maxulysse committed May 28, 2021
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Commits on May 30, 2021

  1. fix: output

    @maxulysse
    maxulysse committed May 30, 2021
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  2. feat: simplify tests

    @maxulysse
    maxulysse committed May 30, 2021
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  3. fix: tests

    @maxulysse
    maxulysse committed May 30, 2021
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Commits on Jun 3, 2021

  1. feat: simplify test profiles

    @maxulysse
    maxulysse committed Jun 3, 2021
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  2. feat: refactor + reorganize modules

    @maxulysse
    maxulysse committed Jun 3, 2021
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  3. feat: refactor - forgot to commit file

    @maxulysse
    maxulysse committed Jun 3, 2021
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Commits on Jun 4, 2021

  1. fix: gatk4/markduplicatesspark

    @maxulysse
    maxulysse committed Jun 4, 2021
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Commits on Jun 7, 2021

  1. fix: subworfklow tests

    @maxulysse
    maxulysse committed Jun 7, 2021
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  2. fix: markduplicats tests

    @maxulysse
    maxulysse committed Jun 7, 2021
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  3. feat: update bwa/bwamem2 modules

    @maxulysse
    maxulysse committed Jun 7, 2021
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  4. feat: update trimgalore

    @maxulysse
    maxulysse committed Jun 7, 2021
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  5. feat: update tabix/tabix

    @maxulysse
    maxulysse committed Jun 7, 2021
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  6. feat: update and add strelka modules

    @maxulysse
    maxulysse committed Jun 7, 2021
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  7. fix: typo

    @maxulysse
    maxulysse committed Jun 7, 2021
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  8. fix: path to module

    @maxulysse
    maxulysse committed Jun 7, 2021
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  9. fix: typo

    @maxulysse
    maxulysse committed Jun 7, 2021
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  10. feat: update samtools/merge

    @maxulysse
    maxulysse committed Jun 7, 2021
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  11. feat: update multiqc modules

    @maxulysse
    maxulysse committed Jun 7, 2021
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  12. feat: replace msisensor by msisensor-pro

    @maxulysse
    maxulysse committed Jun 7, 2021
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  13. fix: path to modules

    @maxulysse
    maxulysse committed Jun 7, 2021
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  14. fix: msisensor-pro test

    @maxulysse
    maxulysse committed Jun 7, 2021
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  15. fix: msisensorpro execution7

    @maxulysse
    maxulysse committed Jun 7, 2021
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  16. feat: code polishing

    @maxulysse
    maxulysse committed Jun 7, 2021
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  17. fix: improve csv files generation

    @maxulysse
    maxulysse committed Jun 7, 2021
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  18. feat: code polishing

    @maxulysse
    maxulysse committed Jun 7, 2021
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  19. fix: update CI

    @maxulysse
    maxulysse committed Jun 7, 2021
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  20. fix: add csv for recalibrated bam files

    @maxulysse
    maxulysse committed Jun 7, 2021
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  21. feat: restart from all steps

    @maxulysse
    maxulysse committed Jun 7, 2021
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Commits on Jun 8, 2021

  1. fix: gatk4spark tests

    @maxulysse
    maxulysse committed Jun 8, 2021
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  2. feat: code polishing

    @maxulysse
    maxulysse committed Jun 8, 2021
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