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Changes needed for scaling up and running in Terra #1

Merged
merged 74 commits into from
Feb 2, 2024
Merged

Changes needed for scaling up and running in Terra #1

merged 74 commits into from
Feb 2, 2024

Commits on Jun 15, 2023

  1. testing dockerhub for terra

    @meganshand
    meganshand committed Jun 15, 2023
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Commits on Jun 16, 2023

  1. dockers

    @meganshand
    meganshand committed Jun 16, 2023
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Commits on Aug 2, 2023

  1. workaround for disk bug

    @meganshand
    meganshand committed Aug 2, 2023
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Commits on Aug 3, 2023

  1. making cpu input for CrosscheckFingerprint

    @meganshand
    meganshand committed Aug 3, 2023
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  2. trying fixed vm size

    @meganshand
    meganshand committed Aug 3, 2023
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  3. new mcahine type

    @meganshand
    meganshand committed Aug 3, 2023
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  4. some changes

    @meganshand
    meganshand committed Aug 3, 2023
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  5. trying osmething

    @meganshand
    meganshand committed Aug 3, 2023
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  6. trying different family

    @meganshand
    meganshand committed Aug 3, 2023
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Commits on Aug 4, 2023

  1. another vm

    @meganshand
    meganshand committed Aug 4, 2023
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  2. switching all VMs to E

    @meganshand
    meganshand committed Aug 4, 2023
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Commits on Aug 24, 2023

  1. removing family size

    @meganshand
    meganshand committed Aug 24, 2023
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Commits on Aug 25, 2023

  1. testing gendb from gatk 

    updating gatk docker

adding sas token

fixing headeer vcf

header index
    @meganshand
    meganshand committed Aug 25, 2023
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  2. adding max stream size env variable

    @meganshand
    meganshand committed Aug 25, 2023
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  3. trying new branch from genDB

    @meganshand
    meganshand committed Aug 25, 2023
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Commits on Aug 30, 2023

  1. changing to Azure dockers

    @meganshand
    meganshand committed Aug 30, 2023
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Commits on Aug 31, 2023

  1. adding maxRetries

    @meganshand
    meganshand committed Aug 31, 2023
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Commits on Sep 22, 2023

  1. switching back to DockerHub for call caching

    @meganshand
    meganshand committed Sep 22, 2023
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Commits on Oct 10, 2023

  1. testing gather

    @meganshand
    meganshand committed Oct 10, 2023
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  2. fixing

    @meganshand
    meganshand committed Oct 10, 2023
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Commits on Oct 11, 2023

  1. streaming gather of vcfs

    @meganshand
    meganshand committed Oct 11, 2023
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  2. more testing of gather

    @meganshand
    meganshand committed Oct 11, 2023
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Commits on Oct 13, 2023

  1. fixing fingerprint issues

    @meganshand
    meganshand committed Oct 13, 2023
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  2. new version of GenomcisDB

    @meganshand
    meganshand committed Oct 13, 2023
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Commits on Oct 20, 2023

  1. fixing crosscheck fingerprints

    @meganshand
    meganshand committed Oct 20, 2023
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  2. comment

    @meganshand
    meganshand committed Oct 20, 2023
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  3. cleanup

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

  1. typo

    @meganshand
    meganshand committed Oct 23, 2023
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  2. sas token encoding/decoding

    @meganshand
    meganshand committed Oct 23, 2023
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Commits on Oct 24, 2023

  1. updaing docker

    @meganshand
    meganshand committed Oct 24, 2023
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  2. typo

    @meganshand
    meganshand committed Oct 24, 2023
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  3. sas

    @meganshand
    meganshand committed Oct 24, 2023
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Commits on Oct 27, 2023

  1. fixing scattered fingerprinting

    @meganshand
    meganshand committed Oct 27, 2023
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  2. don't localize selectVariants for Fingerprinting

    @meganshand
    meganshand committed Oct 27, 2023
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  3. fixing partitioning

    @meganshand
    meganshand committed Oct 27, 2023
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Commits on Nov 16, 2023

  1. trying new sas feature on import only

    @meganshand
    meganshand committed Nov 16, 2023
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  2. debugging

    @meganshand
    meganshand committed Nov 16, 2023
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  3. removing debug print line

    @meganshand
    meganshand committed Nov 16, 2023
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Commits on Nov 21, 2023

  1. revertting back for now

    @meganshand
    meganshand committed Nov 21, 2023
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  2. forgot a change

    @meganshand
    meganshand committed Nov 21, 2023
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  3. changing input array to fofn

    @meganshand
    meganshand committed Nov 21, 2023
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Commits on Nov 22, 2023

  1. fixing header_vcf

    @meganshand
    meganshand committed Nov 22, 2023
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  2. splitting fofn reading

    @meganshand
    meganshand committed Nov 22, 2023
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Commits on Dec 1, 2023

  1. sas environment variable

    @meganshand
    meganshand committed Dec 1, 2023
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  2. debugging

    @meganshand
    meganshand committed Dec 1, 2023
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Commits on Dec 8, 2023

  1. trying sas for gatk

    @meganshand
    meganshand committed Dec 8, 2023
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  2. adding fofns

    @meganshand
    meganshand committed Dec 8, 2023
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  3. fixing quotes

    @meganshand
    meganshand committed Dec 8, 2023
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Commits on Dec 11, 2023

  1. quotes?

    @meganshand
    meganshand committed Dec 11, 2023
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  2. update gatk for gather

    @meganshand
    meganshand committed Dec 11, 2023
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Commits on Dec 12, 2023

  1. testing new jar

    @meganshand
    meganshand committed Dec 12, 2023
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  2. question mark?

    @meganshand
    meganshand committed Dec 12, 2023
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Commits on Dec 13, 2023

  1. fixing fingerprinting

    @meganshand
    meganshand committed Dec 13, 2023
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  2. fix

    @meganshand
    meganshand committed Dec 13, 2023
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  3. typo

    @meganshand
    meganshand committed Dec 13, 2023
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  4. trying new jar for fingerprinting

    @meganshand
    meganshand committed Dec 13, 2023
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  5. no more max retries

    @meganshand
    meganshand committed Dec 13, 2023
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  6. removing temp inputs

    @meganshand
    meganshand committed Dec 13, 2023
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  7. removing debugging outputs from fingerprinting

    @meganshand
    meganshand committed Dec 13, 2023
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Commits on Dec 14, 2023

  1. adding back retries

    @meganshand
    meganshand committed Dec 14, 2023
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Commits on Dec 15, 2023

  1. more retries

    @meganshand
    meganshand committed Dec 15, 2023
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Commits on Dec 18, 2023

  1. more maxRetries

    @meganshand
    meganshand committed Dec 18, 2023
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  2. switching to gatk 4.5.0.0

    @meganshand
    meganshand committed Dec 18, 2023
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Commits on Dec 19, 2023

  1. removing test wdl

    @meganshand
    meganshand committed Dec 19, 2023
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Commits on Jan 30, 2024

  1. untested - addressing comments

    @meganshand
    meganshand committed Jan 30, 2024
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Commits on Jan 31, 2024

  1. changing default scatter_mode to necessary option for 15k samples

    @meganshand
    meganshand committed Jan 31, 2024
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  2. updating example inputs

    @meganshand
    meganshand committed Jan 31, 2024
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  3. fixed typo

    @meganshand
    meganshand committed Jan 31, 2024
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  4. fixing regex

    @meganshand
    meganshand committed Jan 31, 2024
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  5. swapped url order

    @meganshand
    meganshand committed Jan 31, 2024
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  6. fixing index files

    @meganshand
    meganshand committed Jan 31, 2024
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  7. trying more sed to fix index

    @meganshand
    meganshand committed Jan 31, 2024
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Commits on Feb 2, 2024

  1. fixing sed

    @meganshand
    meganshand committed Feb 2, 2024
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  2. clean up sed in fingerprinting now that we generate gvcf list from sa… 

    …mple_map
    @meganshand
    meganshand committed Feb 2, 2024
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