Code

Staging -> Master#837

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nikellepetrillo merged 90 commits intomasterbroadinstitute/warp:masterfrom stagingbroadinstitute/warp:stagingCopy head branch name to clipboardNov 10, 2022

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Commits

Commits on Jul 15, 2022

• Increase disk size for MakeOptionalBam for Ultima pipeline (#766)

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  meganshand

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  nikellepetrillo

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• Update WGS README.md (#770)

  ekiernan

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Commits on Jul 20, 2022

• Correct run example command (#776)

  timaeusx

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• update plumbing json (#773)

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Commits on Jul 26, 2022

• rebuild star docker image (#775)

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Commits on Jul 27, 2022

• Remove redundant Picard Dockerfile and directory (#778)

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• Add section to Docker style guide for compiling on M series Macs and other ARM machines and fix typos (#777)

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• Migrate Skylab samtools to Broad samtools (#779)

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Commits on Aug 1, 2022

• Cleanup dropseq_tools related files (#780)

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Commits on Aug 2, 2022

• Increase memory in fastp and GroupByUMIs tasks (#698)

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Commits on Aug 3, 2022

• Update imputation bcf/vcftools and minimac4 docker images (#787)

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Commits on Aug 9, 2022

• Rebuild trim adapters docker image (#789)

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• Rename trim-adapters docker directory to ea-utils (#793)

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Commits on Aug 10, 2022

• Remove unused subread docker directory (#794)

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Commits on Aug 11, 2022

• Update BuildIntervalList to use samtools docker image (#791)

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Commits on Aug 12, 2022

• Remove unused HCA_post_processing docker directory (#795)

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Commits on Aug 16, 2022

• Remove unused subset-fastq-dataset docker directory (#796)

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Commits on Aug 17, 2022

• Consolidate Python script dockers into a single docker image (#797)

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Commits on Aug 18, 2022

• moving scientific ownership to sam lee instead of laura (#790)

  nikellepetrillo

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• add filter to inputFileNames (#800)

  nikellepetrillo

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Commits on Aug 19, 2022

• Split off BWA docker files from snaptools docker (#799)

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Commits on Aug 24, 2022

• Pytools related cleanup (#802)

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Commits on Aug 26, 2022

• Rebuild bcf/vcftools and minimac dockers (#803)

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Commits on Aug 29, 2022

• update get_changed_pipeline_worklow_test_args.sh (#806)

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  nikellepetrillo

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• update tasks with new docker image, update calls to ingesttotdr task with additionally added required parameter

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Commits on Aug 31, 2022

• KM update WGS pipeline docs (#811)

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  kayleemathews

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Commits on Sep 1, 2022

• Rebuild featureCounts image into a general subread image (#810)

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• Merge branch 'develop' into BroadInternalArraysImputation

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Commits on Sep 2, 2022

• update pipeline_version to match changelog version

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• Merge branch 'BroadInternalArraysImputation' of github.com:broadinstitute/warp into BroadInternalArraysImputation

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• make arrays ingest only once to tdr for all samples

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• tesing out optional array outputs

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• update with new docker

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• update changelogs'

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• make workflow outputs also arrays

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• change outputs from [File]? to [File?]

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• change internal arrays task to also have Array[File?]

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• add optional values for arrays to workflow level inputs

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• edit optiona ? to inside brackets

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• make optional inputs as required

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Commits on Sep 3, 2022

• remove call to ingest outputs into dataset

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• remove call to trigger PRS

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• revert changing the Arrays pipeline to handle array inputs back to single sample

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• Merge branch 'develop' of github.com:broadinstitute/warp into develop

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Commits on Sep 6, 2022

• Update tasks using plain ubuntu images to use alpine (#813)

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• Add troubleshooting note to docker directory readme file (#814)

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• Merge branch 'develop' into BroadInternalArraysImputation

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• set imputation back to original

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• Merge branch 'BroadInternalArraysImputation' of github.com:broadinstitute/warp into BroadInternalArraysImputation

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• Merge branch 'develop' of github.com:broadinstitute/warp into develop

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• update pipeline_version to match changelog version

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• make arrays ingest only once to tdr for all samples

  schaluva

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  87625f0

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• tesing out optional array outputs

  schaluva

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  37039e7

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• update with new docker

  schaluva

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• update changelogs'

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• make workflow outputs also arrays

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• change outputs from [File]? to [File?]

  schaluva

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• change internal arrays task to also have Array[File?]

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• add optional values for arrays to workflow level inputs

  schaluva

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  e9d5295

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• edit optiona ? to inside brackets

  schaluva

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  c68a2fd

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• make optional inputs as required

  schaluva

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  b22a006

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• remove call to ingest outputs into dataset

  schaluva

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  153b381

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• remove call to trigger PRS

  schaluva

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  6884ab2

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• revert changing the Arrays pipeline to handle array inputs back to single sample

  schaluva

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  1a31f39

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• set imputation back to original

  schaluva

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• Merge branch 'BroadInternalArraysImputation' of github.com:broadinstitute/warp into BroadInternalArraysImputation

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Commits on Sep 7, 2022

• update change logs

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• remove new versions and add updates to existing version with new commit date

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• Merge pull request #808 from broadinstitute/BroadInternalArraysImputation

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  schaluva

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• double quotes weirdly unsupported in changelogs :( (#817)

  jessicaway

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Commits on Sep 9, 2022

• add the skylab tests to the pr tests/nightly tests (#816)

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  nikellepetrillo

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• added updated WARP email for all pipelines (#819)

  ekiernan

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Commits on Sep 12, 2022

• GL-2053: Rebuild HISAT2 docker (#821)

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  timaeusx

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Commits on Sep 13, 2022

• Build new RSEM docker image, supporting files, and update tasks, changelogs, and version numbers (#822)

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Commits on Sep 16, 2022

• GL-2059: Update testing UI in Jenkins (#824)

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Commits on Sep 20, 2022

• change from dockerhub to gcr

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• update changelogs

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Commits on Sep 21, 2022

• GL-2003: Remove /cromwell_root/ prefix in UGWGG task output file paths (#829)

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• GL-2017: Docker directory consistency improvements and general cleanup (#827)

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• Merge branch 'develop' into emerge_gcr_images

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Commits on Sep 22, 2022

• GL-2055: Updated Build_indices container and Fixes on corresponding WDL (#830)

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• Merge branch 'develop' into emerge_gcr_images

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Commits on Sep 26, 2022

• Security updates for Picard-Python, BCFTools/VCFTools, and Minimac4 (#833)

  timaeusx

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• added disk memory and cpu to each task as input (#832)

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Commits on Sep 30, 2022

• Merge branch 'develop' into emerge_gcr_images

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• update arrays changelog

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• arrays changelogs updated with gcr image

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• update changelogs

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• Merge pull request #828 from broadinstitute/emerge_gcr_images

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Commits on Oct 5, 2022

• Merge pull request #834 from broadinstitute/develop

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