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feat: deduplicate with UMIs #1358

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feat: deduplicate with UMIs #1358

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Commits on Oct 20, 2023

  1. restructure fastp trim for TGA to extract UMIs into tags instead of h… 

    …eadername
    @mathiasbio
    mathiasbio committed Oct 20, 2023
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  2. divided alignment in two

    @mathiasbio
    mathiasbio committed Oct 20, 2023
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Commits on Oct 23, 2023

  1. add gzip to interleaved umi trimmed fastqs

    @mathiasbio
    mathiasbio committed Oct 23, 2023
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  2. remove detect adapters for pe in fastp

    @mathiasbio
    mathiasbio committed Oct 23, 2023
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Commits on Nov 1, 2023

  1. add rule sleep before starting analysis

    @mathiasbio
    mathiasbio committed Nov 1, 2023
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Commits on Dec 12, 2023

  1. merge release13

    @mathiasbio
    mathiasbio committed Dec 12, 2023
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  2. add extra rule to PON workflow

    @mathiasbio
    mathiasbio committed Dec 12, 2023
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Commits on Jan 4, 2024

  1. merge release 13

    @mathiasbio
    mathiasbio committed Jan 4, 2024
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  2. increase time to 200 sec

    @mathiasbio
    mathiasbio committed Jan 4, 2024
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  3. add sleep requirement to concatenate umi

    @mathiasbio
    mathiasbio committed Jan 4, 2024
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Commits on Jan 15, 2024

  1. fix qc workflow

    @mathiasbio
    mathiasbio committed Jan 15, 2024
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Commits on Jan 16, 2024

  1. fix merge conflict

    @mathiasbio
    mathiasbio committed Jan 16, 2024
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  2. add new rules and functionality to create consensus reads in dedup

    @mathiasbio
    mathiasbio committed Jan 16, 2024
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  3. fix bugs

    @mathiasbio
    mathiasbio committed Jan 16, 2024
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  4. hardcode new version of sentieon

    @mathiasbio
    mathiasbio committed Jan 16, 2024
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Commits on Jan 17, 2024

  1. remove failing env variable assignment

    @mathiasbio
    mathiasbio committed Jan 17, 2024
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  2. remove env in umi rule

    @mathiasbio
    mathiasbio committed Jan 17, 2024
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Commits on Jan 18, 2024

  1. fix header

    @mathiasbio
    mathiasbio committed Jan 18, 2024
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  2. fix bug

    @mathiasbio
    mathiasbio committed Jan 18, 2024
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  3. fix header command

    @mathiasbio
    mathiasbio committed Jan 18, 2024
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Commits on Jan 19, 2024

  1. fix bugs

    @mathiasbio
    mathiasbio committed Jan 19, 2024
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  2. fix bug

    @mathiasbio
    mathiasbio committed Jan 19, 2024
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Commits on Apr 15, 2024

  1. merge develop

    @mathiasbio
    mathiasbio committed Apr 15, 2024
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  2. fix changelog

    @mathiasbio
    mathiasbio committed Apr 15, 2024
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  3. add sampletype

    @mathiasbio
    mathiasbio committed Apr 15, 2024
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  4. Merge branch 'deduplicate_with_umi' of github.com:Clinical-Genomics/B… 

    …ALSAMIC into deduplicate_with_umi
    @mathiasbio
    mathiasbio committed Apr 15, 2024
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Commits on Apr 16, 2024

  1. update version

    @mathiasbio
    mathiasbio committed Apr 16, 2024
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  2. Merge branch 'deduplicate_with_umi' of github.com:Clinical-Genomics/B… 

    …ALSAMIC into deduplicate_with_umi
    @mathiasbio
    mathiasbio committed Apr 16, 2024
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  3. Merge branch 'deduplicate_with_umi' of github.com:Clinical-Genomics/B… 

    …ALSAMIC into deduplicate_with_umi
    @mathiasbio
    mathiasbio committed Apr 16, 2024
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  4. add new output files

    @mathiasbio
    mathiasbio committed Apr 16, 2024
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  5. Merge branch 'deduplicate_with_umi' of github.com:Clinical-Genomics/B… 

    …ALSAMIC into deduplicate_with_umi
    @mathiasbio
    mathiasbio committed Apr 16, 2024
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  6. remove arguments

    @mathiasbio
    mathiasbio committed Apr 16, 2024
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  7. add merge bam step

    @mathiasbio
    mathiasbio committed Apr 16, 2024
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Commits on May 2, 2024

  1. add base quality cap script to TGA workflow

    @mathiasbio
    mathiasbio committed May 2, 2024
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  2. switch container

    @mathiasbio
    mathiasbio committed May 2, 2024
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  3. fix bug

    @mathiasbio
    mathiasbio committed May 2, 2024
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  4. bug fix

    @mathiasbio
    mathiasbio committed May 2, 2024
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  5. bug fix

    @mathiasbio
    mathiasbio committed May 2, 2024
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Commits on May 3, 2024

  1. test switching UMI tag to RX instead of XR

    @mathiasbio
    mathiasbio committed May 3, 2024
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Commits on May 6, 2024

  1. merge fastqs

    @mathiasbio
    mathiasbio committed May 6, 2024
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  2. bug fix

    @mathiasbio
    mathiasbio committed May 6, 2024
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  3. add concatenation

    @mathiasbio
    mathiasbio committed May 6, 2024
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Commits on May 8, 2024

  1. fix bug

    @mathiasbio
    mathiasbio committed May 8, 2024
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  2. bug

    @mathiasbio
    mathiasbio committed May 8, 2024
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Commits on May 14, 2024

  1. go back to parallel trimming

    @mathiasbio
    mathiasbio committed May 14, 2024
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  2. add picard fixmate

    @mathiasbio
    mathiasbio committed May 14, 2024
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  3. revert back to concatenating fastqs

    @mathiasbio
    mathiasbio committed May 14, 2024
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Commits on May 15, 2024

  1. nothing

    @mathiasbio
    mathiasbio committed May 15, 2024
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Commits on May 29, 2024

  1. update multiqc to 1.22.1

    @mathiasbio
    mathiasbio committed May 29, 2024
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  2. update version in docs

    @mathiasbio
    mathiasbio committed May 29, 2024
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  3. removed sed command

    @mathiasbio
    mathiasbio committed May 29, 2024
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  4. changelog

    @mathiasbio
    mathiasbio committed May 29, 2024
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Commits on May 30, 2024

  1. add separate multiqc container

    @mathiasbio
    mathiasbio committed May 30, 2024
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  2. remove multiqc from align sif

    @mathiasbio
    mathiasbio committed May 30, 2024
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  3. add build to actions

    @mathiasbio
    mathiasbio committed May 30, 2024
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  4. add test script

    @mathiasbio
    mathiasbio committed May 30, 2024
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  5. update which container to use

    @mathiasbio
    mathiasbio committed May 30, 2024
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  6. temporary alignqc sif

    @mathiasbio
    mathiasbio committed May 30, 2024
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  7. return align sif name

    @mathiasbio
    mathiasbio committed May 30, 2024
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  8. rework QC steps and add samtools fixmate and collate

    @mathiasbio
    mathiasbio committed May 30, 2024
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  9. Merge branch 'update_multiqc' into deduplicate_with_umi

    @mathiasbio
    mathiasbio committed May 30, 2024
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  10. bug fix

    @mathiasbio
    mathiasbio committed May 30, 2024
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  11. fix

    @mathiasbio
    mathiasbio committed May 30, 2024
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  12. fix

    @mathiasbio
    mathiasbio committed May 30, 2024
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  13. fix

    @mathiasbio
    mathiasbio committed May 30, 2024
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Commits on May 31, 2024

  1. fix

    @mathiasbio
    mathiasbio committed May 31, 2024
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  2. fix

    @mathiasbio
    mathiasbio committed May 31, 2024
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  3. fix outputdir

    @mathiasbio
    mathiasbio committed May 31, 2024
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  4. fix

    @mathiasbio
    mathiasbio committed May 31, 2024
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  5. fix

    @mathiasbio
    mathiasbio committed May 31, 2024
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  6. switch bam for vardict

    @mathiasbio
    mathiasbio committed May 31, 2024
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  7. fix

    @mathiasbio
    mathiasbio committed May 31, 2024
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  8. bug fix

    @mathiasbio
    mathiasbio committed May 31, 2024
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  9. fix

    @mathiasbio
    mathiasbio committed May 31, 2024
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  10. fix

    @mathiasbio
    mathiasbio committed May 31, 2024
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  11. attempting downgrade to 1.18 to fix somalier issue

    @mathiasbio
    mathiasbio committed May 31, 2024
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Commits on Jun 3, 2024

  1. update multiqc to 1.22.2

    @mathiasbio
    mathiasbio committed Jun 3, 2024
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  2. fix

    @mathiasbio
    mathiasbio committed Jun 3, 2024
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  3. go back to version 1.18

    @mathiasbio
    mathiasbio committed Jun 3, 2024
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  4. change collect qc metrics sample id parsing

    @mathiasbio
    mathiasbio committed Jun 3, 2024
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  5. split up sort rule

    @mathiasbio
    mathiasbio committed Jun 3, 2024
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  6. switch from sentieon to samtools

    @mathiasbio
    mathiasbio committed Jun 3, 2024
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  7. bug fix

    @mathiasbio
    mathiasbio committed Jun 3, 2024
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  8. set tmpdirs

    @mathiasbio
    mathiasbio committed Jun 3, 2024
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  9. black

    @mathiasbio
    mathiasbio committed Jun 3, 2024
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  10. updated changelog

    @mathiasbio
    mathiasbio committed Jun 3, 2024
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  11. fix pytest

    @mathiasbio
    mathiasbio committed Jun 3, 2024
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  12. Merge branch 'develop' of github.com:Clinical-Genomics/BALSAMIC into … 

    …develop
    @mathiasbio
    mathiasbio committed Jun 3, 2024
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  13. Merge branch 'develop' into update_multiqc

    @mathiasbio
    mathiasbio committed Jun 3, 2024
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  14. move out qc metrics to separate rule

    @mathiasbio
    mathiasbio committed Jun 3, 2024
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  15. Merge branch 'update_multiqc' of github.com:Clinical-Genomics/BALSAMI… 

    …C into update_multiqc
    @mathiasbio
    mathiasbio committed Jun 3, 2024
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  16. Merge branch 'update_multiqc' into deduplicate_with_umi

    @mathiasbio
    mathiasbio committed Jun 3, 2024
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  17. only use capped qual for manta

    @mathiasbio
    mathiasbio committed Jun 3, 2024
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  18. fix

    @mathiasbio
    mathiasbio committed Jun 3, 2024
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  19. fix

    @mathiasbio
    mathiasbio committed Jun 3, 2024
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  20. fix

    @mathiasbio
    mathiasbio committed Jun 3, 2024
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  21. divide up SV rules into separate workflows

    @mathiasbio
    mathiasbio committed Jun 3, 2024
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  22. fix

    @mathiasbio
    mathiasbio committed Jun 3, 2024
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  23. add rules

    @mathiasbio
    mathiasbio committed Jun 3, 2024
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Commits on Jun 4, 2024

  1. clean up

    @mathiasbio
    mathiasbio committed Jun 4, 2024
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  2. rename

    @mathiasbio
    mathiasbio committed Jun 4, 2024
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  3. wgs qc fix

    @mathiasbio
    mathiasbio committed Jun 4, 2024
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Commits on Jun 5, 2024

  1. fix bugs

    @mathiasbio
    mathiasbio committed Jun 5, 2024
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  2. fix temp

    @mathiasbio
    mathiasbio committed Jun 5, 2024
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  3. add index

    @mathiasbio
    mathiasbio committed Jun 5, 2024
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  4. fix

    @mathiasbio
    mathiasbio committed Jun 5, 2024
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Commits on Jun 10, 2024

  1. fix

    @mathiasbio
    mathiasbio committed Jun 10, 2024
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  2. fix

    @mathiasbio
    mathiasbio committed Jun 10, 2024
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  3. fix

    @mathiasbio
    mathiasbio committed Jun 10, 2024
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Commits on Jun 12, 2024

  1. clean up umi trimming

    @mathiasbio
    mathiasbio committed Jun 12, 2024
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  2. black and fix

    @mathiasbio
    mathiasbio committed Jun 12, 2024
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  3. add fastp adapter trimming before UMI extraction

    @mathiasbio
    mathiasbio committed Jun 12, 2024
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  4. fix clean up

    @mathiasbio
    mathiasbio committed Jun 12, 2024
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  5. fix

    @mathiasbio
    mathiasbio committed Jun 12, 2024
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  6. fix pon

    @mathiasbio
    mathiasbio committed Jun 12, 2024
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  7. fix

    @mathiasbio
    mathiasbio committed Jun 12, 2024
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  8. fix

    @mathiasbio
    mathiasbio committed Jun 12, 2024
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  9. fix

    @mathiasbio
    mathiasbio committed Jun 12, 2024
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Commits on Jun 13, 2024

  1. fix

    @mathiasbio
    mathiasbio committed Jun 13, 2024
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Commits on Jun 20, 2024

  1. restructure UMI workflow to use TGA rules where possible

    @mathiasbio
    mathiasbio committed Jun 20, 2024
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  2. fix

    @mathiasbio
    mathiasbio committed Jun 20, 2024
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  3. fix

    @mathiasbio
    mathiasbio committed Jun 20, 2024
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  4. fix

    @mathiasbio
    mathiasbio committed Jun 20, 2024
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  5. fix

    @mathiasbio
    mathiasbio committed Jun 20, 2024
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  6. fix

    @mathiasbio
    mathiasbio committed Jun 20, 2024
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  7. fix

    @mathiasbio
    mathiasbio committed Jun 20, 2024
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Commits on Jun 27, 2024

  1. Merge branch 'develop' of github.com:Clinical-Genomics/BALSAMIC into … 

    …develop
    @mathiasbio
    mathiasbio committed Jun 27, 2024
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Commits on Jul 3, 2024

  1. merge develop

    @mathiasbio
    mathiasbio committed Jul 3, 2024
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  2. Merge branch 'develop' of github.com:Clinical-Genomics/BALSAMIC into … 

    …develop
    @mathiasbio
    mathiasbio committed Jul 3, 2024
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  3. merge develop

    @mathiasbio
    mathiasbio committed Jul 3, 2024
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  4. fix merge conflict

    @mathiasbio
    mathiasbio committed Jul 3, 2024
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  5. fix merge conflict

    @mathiasbio
    mathiasbio committed Jul 3, 2024
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  6. change sent env to model

    @mathiasbio
    mathiasbio committed Jul 3, 2024
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  7. same

    @mathiasbio
    mathiasbio committed Jul 3, 2024
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Commits on Jul 4, 2024

  1. black

    @mathiasbio
    mathiasbio committed Jul 4, 2024
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  2. clean up

    @mathiasbio
    mathiasbio committed Jul 4, 2024
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  3. fixing errors

    @mathiasbio
    mathiasbio committed Jul 4, 2024
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Commits on Jul 5, 2024

  1. fix bugs

    @mathiasbio
    mathiasbio committed Jul 5, 2024
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  2. tests fix

    @mathiasbio
    mathiasbio committed Jul 5, 2024
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  3. tests

    @mathiasbio
    mathiasbio committed Jul 5, 2024
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  4. remove quality trim from umi workflow

    @mathiasbio
    mathiasbio committed Jul 5, 2024
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  5. fix

    @mathiasbio
    mathiasbio committed Jul 5, 2024
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  6. lines

    @mathiasbio
    mathiasbio committed Jul 5, 2024
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  7. refactor

    @mathiasbio
    mathiasbio committed Jul 5, 2024
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  8. clean up

    @mathiasbio
    mathiasbio committed Jul 5, 2024
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  9. add sleep to msi rule

    @mathiasbio
    mathiasbio committed Jul 5, 2024
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  10. fix pon workflow

    @mathiasbio
    mathiasbio committed Jul 5, 2024
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  11. add sleep to PON

    @mathiasbio
    mathiasbio committed Jul 5, 2024
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Commits on Jul 8, 2024

  1. remove extra dedup for percent duplicates

    @mathiasbio
    mathiasbio committed Jul 8, 2024
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  2. divide manta germline into 2 workflows

    @mathiasbio
    mathiasbio committed Jul 8, 2024
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Commits on Jul 9, 2024

  1. start documentation

    @mathiasbio
    mathiasbio committed Jul 9, 2024
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  2. code review

    @mathiasbio
    mathiasbio committed Jul 9, 2024
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  3. update cap base quality

    @mathiasbio
    mathiasbio committed Jul 9, 2024
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  4. code review

    @mathiasbio
    mathiasbio committed Jul 9, 2024
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  5. add qc models

    @mathiasbio
    mathiasbio committed Jul 9, 2024
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  6. fix tests

    @mathiasbio
    mathiasbio committed Jul 9, 2024
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  7. fix bugs

    @mathiasbio
    mathiasbio committed Jul 9, 2024
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  8. black

    @mathiasbio
    mathiasbio committed Jul 9, 2024
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Commits on Jul 10, 2024

  1. code review

    @mathiasbio
    mathiasbio committed Jul 10, 2024
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  2. add header param

    @mathiasbio
    mathiasbio committed Jul 10, 2024
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  3. black

    @mathiasbio
    mathiasbio committed Jul 10, 2024
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  4. remove duplicate rule

    @mathiasbio
    mathiasbio committed Jul 10, 2024
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  5. fix coverage

    @mathiasbio
    mathiasbio committed Jul 10, 2024
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Commits on Jul 11, 2024

  1. fix

    @mathiasbio
    mathiasbio committed Jul 11, 2024
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  2. update documentation

    @mathiasbio
    mathiasbio committed Jul 11, 2024
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  3. adjust docs

    @mathiasbio
    mathiasbio committed Jul 11, 2024
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Commits on Jul 12, 2024

  1. remove header params

    @mathiasbio
    mathiasbio committed Jul 12, 2024
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Commits on Jul 22, 2024

  1. fix pon final file

    @mathiasbio
    mathiasbio committed Jul 22, 2024
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Commits on Jul 30, 2024

  1. remove duplicate rules refactoring

    @mathiasbio
    mathiasbio committed Jul 30, 2024
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Commits on Aug 8, 2024

  1. fix issues with bam format

    @mathiasbio
    mathiasbio committed Aug 8, 2024
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Commits on Aug 9, 2024

  1. fix

    @mathiasbio
    mathiasbio committed Aug 9, 2024
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  2. fix

    @mathiasbio
    mathiasbio committed Aug 9, 2024
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  3. add more tmp dirs

    @mathiasbio
    mathiasbio committed Aug 9, 2024
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  4. increase speed by sorting before calmd

    @mathiasbio
    mathiasbio committed Aug 9, 2024
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  5. fix

    @mathiasbio
    mathiasbio committed Aug 9, 2024
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Commits on Aug 15, 2024

  1. change umi edit distance to 1

    @mathiasbio
    mathiasbio committed Aug 15, 2024
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