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[Do not merge!] Pseudo PR for first release #5

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[Do not merge!] Pseudo PR for first release #5

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Commits on Sep 18, 2024

  1. updated configuration files

    Tanya Jain committed Sep 18, 2024
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  2. changes in config to account for bam input rather than fasta input

    Tanya Jain committed Sep 18, 2024
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  3. lima demultiplexing added

    Tanya Jain committed Sep 18, 2024
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Commits on Sep 19, 2024

  1. added new module pbmm2 (missing tests for module as of now) - added p… 

    …bmm2 task
    Tanya Jain committed Sep 19, 2024
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Commits on Sep 24, 2024

  1. adding samtools functionality

    Tanya Jain committed Sep 24, 2024
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Commits on Sep 25, 2024

  1. cleaned up samtools functionality

    Tanya Jain committed Sep 25, 2024
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Commits on Oct 8, 2024

  1. some small mem changes to make compatible with docker

    @tanyasarkjain
    tanyasarkjain committed Oct 8, 2024
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  2. adding deepvariant (though still potentially need to resolve singular… 

    …ity issues)
    Tanya Jain committed Oct 8, 2024
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Commits on Oct 21, 2024

  1. added gatk4haplotype caller

    @tanyasarkjain
    tanyasarkjain committed Oct 21, 2024
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Commits on Oct 22, 2024

  1. Update README.md

    @tanyasarkjain
    tanyasarkjain authored Oct 22, 2024
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  2. Add files via upload 

    adding metro map
    @tanyasarkjain
    tanyasarkjain authored Oct 22, 2024
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  3. Update README.md 

    adding image
    @tanyasarkjain
    tanyasarkjain authored Oct 22, 2024
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  4. Add files via upload

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    tanyasarkjain authored Oct 22, 2024
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  5. Update README.md

    @tanyasarkjain
    tanyasarkjain authored Oct 22, 2024
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  6. Add files via upload

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    tanyasarkjain authored Oct 22, 2024
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  7. Update README.md

    @tanyasarkjain
    tanyasarkjain authored Oct 22, 2024
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  8. Update README.md 

    Modified read me
    @tanyasarkjain
    tanyasarkjain authored Oct 22, 2024
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  9. Update README.md

    @tanyasarkjain
    tanyasarkjain authored Oct 22, 2024
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  10. Update README.md

    @tanyasarkjain
    tanyasarkjain authored Oct 22, 2024
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  11. Update README.md

    @tanyasarkjain
    tanyasarkjain authored Oct 22, 2024
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  12. Update README.md

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    tanyasarkjain authored Oct 22, 2024
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  13. Add files via upload

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    tanyasarkjain authored Oct 22, 2024
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Commits on Oct 28, 2024

  1. seperate workfall for bam variant calling

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    tanyasarkjain committed Oct 28, 2024
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Commits on Oct 30, 2024

  1. added regions to deepvariant

    @tanyasarkjain
    tanyasarkjain committed Oct 30, 2024
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  2. deepvariant working on savio cluster (singularity)

    Tanya Jain committed Oct 30, 2024
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Commits on Nov 1, 2024

  1. changes

    @tanyasarkjain
    tanyasarkjain committed Nov 1, 2024
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  2. change

    @tanyasarkjain
    tanyasarkjain committed Nov 1, 2024
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  3. succ run + changing to process_high from process_large

    Tanya Jain committed Nov 1, 2024
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Commits on Nov 5, 2024

  1. trgt workflow

    @tanyasarkjain
    tanyasarkjain committed Nov 5, 2024
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  2. change to fasta

    @tanyasarkjain
    tanyasarkjain committed Nov 5, 2024
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  3. sort

    @tanyasarkjain
    tanyasarkjain committed Nov 5, 2024
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  4. simplified plot functionality

    @tanyasarkjain
    tanyasarkjain committed Nov 5, 2024
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  5. typo

    @tanyasarkjain
    tanyasarkjain committed Nov 5, 2024
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  6. change

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    tanyasarkjain committed Nov 5, 2024
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  7. small change

    @tanyasarkjain
    tanyasarkjain committed Nov 5, 2024
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  8. adding id option

    @tanyasarkjain
    tanyasarkjain committed Nov 5, 2024
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  9. fai

    @tanyasarkjain
    tanyasarkjain committed Nov 5, 2024
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  10. indexing

    @tanyasarkjain
    tanyasarkjain committed Nov 5, 2024
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  11. small config changes

    @tanyasarkjain
    tanyasarkjain committed Nov 5, 2024
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  12. config

    Tanya Jain committed Nov 5, 2024
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  13. new config for wgs

    @tanyasarkjain
    tanyasarkjain committed Nov 5, 2024
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  14. config update

    @tanyasarkjain
    tanyasarkjain committed Nov 5, 2024
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  15. slight changes

    @tanyasarkjain
    tanyasarkjain committed Nov 5, 2024
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  16. changes

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    tanyasarkjain committed Nov 5, 2024
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  17. test

    @tanyasarkjain
    tanyasarkjain committed Nov 5, 2024
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Commits on Nov 7, 2024

  1. changes

    @tanyasarkjain
    tanyasarkjain committed Nov 7, 2024
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  2. files unchanged fix

    @tanyasarkjain
    tanyasarkjain committed Nov 7, 2024
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  3. adding hiphase functionality

    @tanyasarkjain
    tanyasarkjain committed Nov 7, 2024
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Commits on Nov 8, 2024

  1. 1 failure with aws triggering

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    tanyasarkjain committed Nov 8, 2024
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  2. Add files via upload

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  3. Add files via upload

    @tanyasarkjain
    tanyasarkjain authored Nov 8, 2024
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  4. Update README.md

    @tanyasarkjain
    tanyasarkjain authored Nov 8, 2024
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  5. Update README.md

    @tanyasarkjain
    tanyasarkjain authored Nov 8, 2024
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  6. Update README.md

    @tanyasarkjain
    tanyasarkjain authored Nov 8, 2024
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  7. Update README.md

    @tanyasarkjain
    tanyasarkjain authored Nov 8, 2024
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  8. Update CITATIONS.md

    @tanyasarkjain
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  9. Add files via upload

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  10. Update README.md

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    tanyasarkjain authored Nov 8, 2024
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  11. update

    @tanyasarkjain
    tanyasarkjain committed Nov 8, 2024
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  12. merge conflict resolution?

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    tanyasarkjain committed Nov 8, 2024
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  13. small todo resolutions

    @tanyasarkjain
    tanyasarkjain committed Nov 8, 2024
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  14. Update usage.md

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    tanyasarkjain authored Nov 8, 2024
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  15. Update usage.md

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    tanyasarkjain authored Nov 8, 2024
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  16. Update output.md

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    tanyasarkjain authored Nov 8, 2024
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  17. Update README.md

    @tanyasarkjain
    tanyasarkjain authored Nov 8, 2024
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  18. Update README.md

    @tanyasarkjain
    tanyasarkjain authored Nov 8, 2024
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  19. Update pacvar.nf

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  20. Update output.md

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  21. sh be minor changes

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    tanyasarkjain committed Nov 8, 2024
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  22. changing intervals

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    tanyasarkjain committed Nov 8, 2024
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  23. hopefully solved the interval issue

    @tanyasarkjain
    tanyasarkjain committed Nov 8, 2024
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  24. consolidate

    @tanyasarkjain
    tanyasarkjain committed Nov 8, 2024
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  25. seems to be working

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    tanyasarkjain committed Nov 8, 2024
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  26. deleting comment

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    tanyasarkjain committed Nov 8, 2024
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Commits on Nov 9, 2024

  1. delete uneeded files

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    tanyasarkjain committed Nov 9, 2024
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Commits on Nov 10, 2024

  1. changes

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    tanyasarkjain committed Nov 10, 2024
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Commits on Nov 11, 2024

  1. small changes

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    tanyasarkjain committed Nov 11, 2024
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  2. downgraded nf-core

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    tanyasarkjain committed Nov 11, 2024
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  3. all tests passing - still need to resolve warnings

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    tanyasarkjain committed Nov 11, 2024
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Commits on Nov 12, 2024

  1. resolving some errors

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    tanyasarkjain committed Nov 12, 2024
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  2. more changes

    @tanyasarkjain
    tanyasarkjain committed Nov 12, 2024
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  3. Add files via upload

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  4. Update README.md

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    tanyasarkjain authored Nov 12, 2024
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  5. more warning resolutions

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    tanyasarkjain committed Nov 12, 2024
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  6. update

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    tanyasarkjain committed Nov 12, 2024
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  7. working for all trials

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    tanyasarkjain committed Nov 12, 2024
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  8. removing output files for final pipeline first release

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    tanyasarkjain committed Nov 12, 2024
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  9. clean up

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    tanyasarkjain committed Nov 12, 2024
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  10. deleting out dir

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    tanyasarkjain committed Nov 12, 2024
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  11. Merge branch 'master' into pacvar

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  12. small gatk change

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  13. Merge branch 'pacvar' of https://github.com/tanyasarkjain/pacvar into… 

    … pacvar
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  14. change in spacing

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    tanyasarkjain committed Nov 12, 2024
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  15. space change

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  16. space

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Commits on Nov 13, 2024

  1. changing memory

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  2. some changes

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    tanyasarkjain committed Nov 13, 2024
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  3. resetting template to 2.14.0

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  4. tryna upgrade to version 3.0.2

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  5. Template update for nf-core/tools version 3.0.2

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  6. Template update for nf-core/tools version 3.0.2

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    tanyasarkjain committed Nov 13, 2024
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  7. passing all tests version 3.0.2 - yet to try again locally

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  8. syntax error

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    tanyasarkjain committed Nov 13, 2024
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  9. 3.0.2

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  10. updating .nf-core.yml

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    tanyasarkjain committed Nov 13, 2024
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  11. fixed a few upgrade to 3.0.2 issues

    Tanya Jain committed Nov 13, 2024
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  12. some corrections -- still more errors

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  13. working except for the naming which is null at the moment

    Tanya Jain committed Nov 13, 2024
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  14. fixed meta id issue

    Tanya Jain committed Nov 13, 2024
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Commits on Nov 14, 2024

  1. mem test conf

    Tanya Jain committed Nov 14, 2024
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  2. conf changes

    Tanya Jain committed Nov 14, 2024
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  3. pretty, 3.02 and linted

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    tanyasarkjain committed Nov 14, 2024
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  4. no out

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    tanyasarkjain committed Nov 14, 2024
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  5. changed nextflow.config to get rid of custom config

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    tanyasarkjain committed Nov 14, 2024
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  6. increasing memory

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    tanyasarkjain committed Nov 14, 2024
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  7. changing gB

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    tanyasarkjain committed Nov 14, 2024
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  8. increasing cpu further for github actions

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    tanyasarkjain committed Nov 14, 2024
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  9. subset of the data for mem saving

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    tanyasarkjain committed Nov 14, 2024
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  10. smaller

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    tanyasarkjain committed Nov 14, 2024
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  11. modifying config files

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    tanyasarkjain committed Nov 14, 2024
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  12. made dataset much smaller

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    tanyasarkjain committed Nov 14, 2024
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  13. removing test files

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    tanyasarkjain committed Nov 14, 2024
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  14. updated bed

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    tanyasarkjain committed Nov 14, 2024
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  15. removing gatk test and making it a full test

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    tanyasarkjain committed Nov 14, 2024
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  16. pretty

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    tanyasarkjain committed Nov 14, 2024
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Commits on Nov 15, 2024

  1. hope this passes

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  2. some small config changes and removing print statements

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  3. Update README.md

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    tanyasarkjain authored Nov 15, 2024
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  4. Update README.md

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    tanyasarkjain authored Nov 15, 2024
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  5. pretty

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  6. small documentation changes

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    tanyasarkjain committed Nov 15, 2024
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Commits on Nov 21, 2024

  1. Update README.md 

    Co-authored-by: Felix Lenner <[email protected]>
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    tanyasarkjain and fellen31 authored Nov 21, 2024
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  2. Update README.md 

    Co-authored-by: Felix Lenner <[email protected]>
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    tanyasarkjain and fellen31 authored Nov 21, 2024
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  3. Update README.md 

    Co-authored-by: Felix Lenner <[email protected]>
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    tanyasarkjain and fellen31 authored Nov 21, 2024
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  4. Update README.md 

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    tanyasarkjain and fellen31 authored Nov 21, 2024
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  5. Update assets/schema_input.json 

    Co-authored-by: Felix Lenner <[email protected]>
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    tanyasarkjain and fellen31 authored Nov 21, 2024
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  6. resolving review comments

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    tanyasarkjain committed Nov 21, 2024
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  7. Update docs/usage.md 

    Co-authored-by: Felix Lenner <[email protected]>
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    tanyasarkjain and fellen31 authored Nov 21, 2024
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  8. Update docs/usage.md 

    Co-authored-by: Felix Lenner <[email protected]>
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    tanyasarkjain and fellen31 authored Nov 21, 2024
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  9. resolution of more review comments

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    tanyasarkjain committed Nov 21, 2024
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  10. Update conf/test.config 

    Co-authored-by: Felix Lenner <[email protected]>
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    tanyasarkjain and fellen31 authored Nov 21, 2024
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  11. Update conf/test_full.config 

    Co-authored-by: Felix Lenner <[email protected]>
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    tanyasarkjain and fellen31 authored Nov 21, 2024
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  12. Update conf/test_wgs_deepvariant.config 

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    tanyasarkjain and fellen31 authored Nov 21, 2024
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  13. Update nextflow.config 

    Co-authored-by: Felix Lenner <[email protected]>
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    tanyasarkjain and fellen31 authored Nov 21, 2024
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  14. updating the release version from 0.1.0 to 1.0.0

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    tanyasarkjain committed Nov 21, 2024
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  15. Update subworkflows/local/bam_snp_variant_calling/main.nf 

    Co-authored-by: Felix Lenner <[email protected]>
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    tanyasarkjain and fellen31 authored Nov 21, 2024
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  16. fixing mapping error

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    tanyasarkjain committed Nov 21, 2024
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  17. fixing pacvar.nf include alignments

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    tanyasarkjain committed Nov 21, 2024
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