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Include preprocessing #3

Merged
merged 29 commits into from
May 2, 2019
Merged

Include preprocessing #3

merged 29 commits into from
May 2, 2019

Commits on May 1, 2019

  1. update README

    @maxulysse
    maxulysse committed May 1, 2019
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  2. update .travis.yml

    @maxulysse
    maxulysse committed May 1, 2019
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  3. add Jenkinsfile

    @maxulysse
    maxulysse committed May 1, 2019
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  4. update conda environment file

    @maxulysse
    maxulysse committed May 1, 2019
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  5. Merge remote-tracking branch 'upstream/dev' into dev

    @maxulysse
    maxulysse committed May 1, 2019
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Commits on May 2, 2019

  1. update software_version collect

    @maxulysse
    maxulysse committed May 2, 2019
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  2. trying to fix travis CI

    @maxulysse
    maxulysse committed May 2, 2019
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  3. only one env

    @maxulysse
    maxulysse committed May 2, 2019
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  4. remove pip upgrade

    @maxulysse
    maxulysse committed May 2, 2019
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  5. remove lint

    @maxulysse
    maxulysse committed May 2, 2019
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  6. remove lib/SarekUtils.groovy

    @maxulysse
    maxulysse committed May 2, 2019
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  7. add References to .gitignore

    @maxulysse
    maxulysse committed May 2, 2019
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  8. lower case

    @maxulysse
    maxulysse committed May 2, 2019
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  9. remove picard

    @maxulysse
    maxulysse committed May 2, 2019
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  10. improve software versions gathering

    @maxulysse
    maxulysse committed May 2, 2019
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  11. fix docker owner

    @maxulysse
    maxulysse committed May 2, 2019
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  12. update tests

    @maxulysse
    maxulysse committed May 2, 2019
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  13. sort params

    @maxulysse
    maxulysse committed May 2, 2019
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  14. add preprocessing

    @maxulysse
    maxulysse committed May 2, 2019
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  15. improve TSV localisation

    @maxulysse
    maxulysse committed May 2, 2019
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  16. improve multiple TSV

    @maxulysse
    maxulysse committed May 2, 2019
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  17. add parrallelized BaseRecalibrator

    @maxulysse
    maxulysse committed May 2, 2019
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  18. smaller test on travisCI

    @maxulysse
    maxulysse committed May 2, 2019
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  19. try to fix path to data

    @maxulysse
    maxulysse committed May 2, 2019
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  20. include building reference when testing...

    @maxulysse
    maxulysse committed May 2, 2019
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  21. reorganize tests

    @maxulysse
    maxulysse committed May 2, 2019
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  22. reduce memory and cpus

    @maxulysse
    maxulysse committed May 2, 2019
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  23. add tests

    @maxulysse
    maxulysse committed May 2, 2019
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  24. add flowcellLaneFromFastq function

    @maxulysse
    maxulysse committed May 2, 2019
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