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More complete CI #806

Merged
merged 50 commits into from
Nov 4, 2022
Merged

More complete CI #806

merged 50 commits into from
Nov 4, 2022

Commits on Nov 2, 2022

  1. starting to reorganize conf files

    @maxulysse
    maxulysse committed Nov 2, 2022
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  2. fix lint

    @maxulysse
    maxulysse committed Nov 2, 2022
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  3. fix lint

    @maxulysse
    maxulysse committed Nov 2, 2022
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  4. add first tests

    @maxulysse
    maxulysse committed Nov 2, 2022
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  5. fix path

    @maxulysse
    maxulysse committed Nov 2, 2022
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  6. fix workflow

    @maxulysse
    maxulysse committed Nov 2, 2022
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  7. fixing aligner tests

    @maxulysse
    maxulysse committed Nov 2, 2022
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  8. fix aligner tests

    @maxulysse
    maxulysse committed Nov 2, 2022
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  9. update annotation tests

    @maxulysse
    maxulysse committed Nov 2, 2022
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  10. test only with docker for now

    @maxulysse
    maxulysse committed Nov 2, 2022
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  11. testing out adding an extra layer of tags

    @maxulysse
    maxulysse committed Nov 2, 2022
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  12. add info as comments instead

    @maxulysse
    maxulysse committed Nov 2, 2022
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  13. sort files

    @maxulysse
    maxulysse committed Nov 2, 2022
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  14. fix file names

    @maxulysse
    maxulysse committed Nov 2, 2022
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  15. alignement_to_fastq

    @maxulysse
    maxulysse committed Nov 2, 2022
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  16. markduplicates

    @maxulysse
    maxulysse committed Nov 2, 2022
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  17. rename files

    @maxulysse
    maxulysse committed Nov 2, 2022
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  18. prepare_recalibration + recalibrate

    @maxulysse
    maxulysse committed Nov 2, 2022
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Commits on Nov 3, 2022

  1. Merge remote-tracking branch 'upstream/dev' into dev_more_complete_CI

    @maxulysse
    maxulysse committed Nov 3, 2022
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  2. code polish + intervals tests

    @maxulysse
    maxulysse committed Nov 3, 2022
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  3. prettier . -w

    @maxulysse
    maxulysse committed Nov 3, 2022
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  4. recalibrate

    @maxulysse
    maxulysse committed Nov 3, 2022
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  5. trimming

    @maxulysse
    maxulysse committed Nov 3, 2022
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  6. umi

    @maxulysse
    maxulysse committed Nov 3, 2022
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  7. default + trimming | split fastq > fastp

    @maxulysse
    maxulysse committed Nov 3, 2022
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  8. target > intervals

    @maxulysse
    maxulysse committed Nov 3, 2022
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  9. pair > default

    @maxulysse
    maxulysse committed Nov 3, 2022
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  10. cnvkit

    @maxulysse
    maxulysse committed Nov 3, 2022
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  11. controlfreec

    @maxulysse
    maxulysse committed Nov 3, 2022
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  12. more cnvkit

    @maxulysse
    maxulysse committed Nov 3, 2022
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  13. deepvariant

    @maxulysse
    maxulysse committed Nov 3, 2022
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  14. freebayes

    @maxulysse
    maxulysse committed Nov 3, 2022
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  15. haplotypecaller

    @maxulysse
    maxulysse committed Nov 3, 2022
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  16. manta

    @maxulysse
    maxulysse committed Nov 3, 2022
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  17. mpileup + controlfreec

    @maxulysse
    maxulysse committed Nov 3, 2022
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  18. mutect2

    @maxulysse
    maxulysse committed Nov 3, 2022
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  19. msisensorpro + strelka + strelka_bp + tiddit

    @maxulysse
    maxulysse committed Nov 3, 2022
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  20. test with singularity and conda as well

    @maxulysse
    maxulysse committed Nov 3, 2022
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  21. update GHA workflows

    @maxulysse
    maxulysse committed Nov 3, 2022
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  22. remove tags

    @maxulysse
    maxulysse committed Nov 3, 2022
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  23. remove more conda tests

    @maxulysse
    maxulysse committed Nov 3, 2022
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  24. remove more tags

    @maxulysse
    maxulysse committed Nov 3, 2022
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  25. update default

    @maxulysse
    maxulysse committed Nov 3, 2022
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  26. less default tests

    @maxulysse
    maxulysse committed Nov 3, 2022
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  27. less default tests

    @maxulysse
    maxulysse committed Nov 3, 2022
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  28. exclude conda from annotation tests

    @maxulysse
    maxulysse committed Nov 3, 2022
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Commits on Nov 4, 2022

  1. exclude more tests + remove md5sum for some conda tests

    @maxulysse
    maxulysse committed Nov 4, 2022
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  2. more conda md5sum removed

    @maxulysse
    maxulysse committed Nov 4, 2022
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  3. comments

    @maxulysse
    maxulysse committed Nov 4, 2022
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  4. more conda md5sum removed + remove duplicate tests

    @maxulysse
    maxulysse committed Nov 4, 2022
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