Code

dev -> staging#834

Code

Merged

nikellepetrillo merged 89 commits intostagingbroadinstitute/warp:stagingfrom developbroadinstitute/warp:developCopy head branch name to clipboardOct 5, 2022

+2,181-1,811

Commits

Commits on Jul 15, 2022

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

  Show description for bb16808
  

  meganshand

  and

  nikellepetrillo

  authored
  bb16808

• Update WGS README.md (#770)

  ekiernan

  authored
  b6ff260

Commits on Jul 20, 2022

• Correct run example command (#776)

  timaeusx

  authored
  528b2e2

• update plumbing json (#773)

  Show description for b055a88
  timaeusx

  authored
  b055a88

Commits on Jul 26, 2022

• rebuild star docker image (#775)

  Show description for 78d7199
  timaeusx

  authored
  78d7199

Commits on Jul 27, 2022

• Remove redundant Picard Dockerfile and directory (#778)

  timaeusx

  authored
  56a1282

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

  timaeusx

  authored
  cc2fb22

• Migrate Skylab samtools to Broad samtools (#779)

  Show description for 2b77797
  timaeusx

  authored
  2b77797

Commits on Aug 1, 2022

• Cleanup dropseq_tools related files (#780)

  Show description for 8f5310d
  timaeusx

  authored
  8f5310d

Commits on Aug 2, 2022

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

  Show description for 46b0538
  

  3 peopleauthored
  46b0538

Commits on Aug 3, 2022

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

  Show description for 27cbd0a
  timaeusx

  authored
  27cbd0a

Commits on Aug 9, 2022

• Rebuild trim adapters docker image (#789)

  Show description for 8b443fe
  timaeusx

  authored
  8b443fe

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

  timaeusx

  authored
  6461d9f

Commits on Aug 10, 2022

• Remove unused subread docker directory (#794)

  timaeusx

  authored
  e77b4a3

Commits on Aug 11, 2022

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

  Show description for ae70d19
  timaeusx

  authored
  ae70d19

Commits on Aug 12, 2022

• Remove unused HCA_post_processing docker directory (#795)

  timaeusx

  authored
  c523c7c

Commits on Aug 16, 2022

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

  timaeusx

  authored
  37c3584

Commits on Aug 17, 2022

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

  Show description for ced227a
  timaeusx

  authored
  ced227a

Commits on Aug 18, 2022

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

  nikellepetrillo

  authored
  7c27b3d

• add filter to inputFileNames (#800)

  nikellepetrillo

  authored
  b2ad36b

Commits on Aug 19, 2022

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

  Show description for 48febaf
  timaeusx

  authored
  48febaf

Commits on Aug 24, 2022

• Pytools related cleanup (#802)

  Show description for 55876e9
  timaeusx

  authored
  55876e9

Commits on Aug 26, 2022

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

  Show description for 432da2b
  timaeusx

  authored
  432da2b

Commits on Aug 29, 2022

• update get_changed_pipeline_worklow_test_args.sh (#806)

  Show description for 2ab17f5
  nikellepetrillo

  authored
  2ab17f5

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

  schaluva

  committed
  b02c639

Commits on Aug 31, 2022

• KM update WGS pipeline docs (#811)

  Show description for 102eecf
  

  kayleemathews

  and

  ekiernan

  authored
  102eecf

Commits on Sep 1, 2022

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

  Show description for 3ca36b4
  timaeusx

  authored
  3ca36b4

• Merge branch 'develop' into BroadInternalArraysImputation

  schaluva

  authored
  a69aa31

Commits on Sep 2, 2022

• update pipeline_version to match changelog version

  schaluva

  committed
  dedba41

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

  schaluva

  committed
  e688d7f

• make arrays ingest only once to tdr for all samples

  schaluva

  committed
  ff4eae6

• tesing out optional array outputs

  schaluva

  committed
  8a34cc3

• update with new docker

  schaluva

  committed
  08ac5bc

• update changelogs'

  schaluva

  committed
  121804d

• make workflow outputs also arrays

  schaluva

  committed
  6ad46b9

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

  schaluva

  committed
  eca1b9a

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

  schaluva

  committed
  df21621

• add optional values for arrays to workflow level inputs

  schaluva

  committed
  3ef3c5e

• edit optiona ? to inside brackets

  schaluva

  committed
  2e475f9

• make optional inputs as required

  schaluva

  committed
  f68efe9

Commits on Sep 3, 2022

• remove call to ingest outputs into dataset

  schaluva

  committed
  6c76d75

• remove call to trigger PRS

  schaluva

  committed
  3ebe184

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

  schaluva

  committed
  ecbf83a

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

  schaluva

  committed
  8b33257

Commits on Sep 6, 2022

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

  Show description for e46294a
  timaeusx

  authored
  e46294a

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

  Show description for d228be3
  timaeusx

  authored
  d228be3

• Merge branch 'develop' into BroadInternalArraysImputation

  schaluva

  authored
  1e0eba4

• set imputation back to original

  schaluva

  committed
  d996689

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

  schaluva

  committed
  e41f1e3

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

  schaluva

  committed
  a60a96d

• update pipeline_version to match changelog version

  schaluva

  committed
  0faf67c

• make arrays ingest only once to tdr for all samples

  schaluva

  committed
  87625f0

• tesing out optional array outputs

  schaluva

  committed
  37039e7

• update with new docker

  schaluva

  committed
  148b5eb

• update changelogs'

  schaluva

  committed
  e104f95

• make workflow outputs also arrays

  schaluva

  committed
  6ebb61d

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

  schaluva

  committed
  beef899

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

  schaluva

  committed
  bb93aeb

• add optional values for arrays to workflow level inputs

  schaluva

  committed
  e9d5295

• edit optiona ? to inside brackets

  schaluva

  committed
  c68a2fd

• make optional inputs as required

  schaluva

  committed
  b22a006

• remove call to ingest outputs into dataset

  schaluva

  committed
  153b381

• remove call to trigger PRS

  schaluva

  committed
  6884ab2

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

  schaluva

  committed
  1a31f39

• set imputation back to original

  schaluva

  committed
  54d02dd

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

  schaluva

  committed
  c1431f1

Commits on Sep 7, 2022

• update change logs

  schaluva

  committed
  9a81ecd

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

  schaluva

  committed
  137b57c

• Merge pull request #808 from broadinstitute/BroadInternalArraysImputation

  Show description for 81e3897
  schaluva

  authored
  81e3897

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

  jessicaway

  authored
  d7e439c

Commits on Sep 9, 2022

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

  Show description for d8a0315
  nikellepetrillo

  authored
  d8a0315

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

  ekiernan

  authored
  6adc30d

Commits on Sep 12, 2022

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

  Show description for 8cd05da
  timaeusx

  authored
  8cd05da

Commits on Sep 13, 2022

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

  timaeusx

  authored
  bec74de

Commits on Sep 16, 2022

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

  Show description for 2834d0e
  timaeusx

  authored
  2834d0e

Commits on Sep 20, 2022

• change from dockerhub to gcr

  schaluva

  committed
  2ce31b0

• update changelogs

  schaluva

  committed
  b6ee9b8

Commits on Sep 21, 2022

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

  Show description for 8856e37
  timaeusx

  authored
  8856e37

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

  Show description for 83c3ab7
  timaeusx

  authored
  83c3ab7

• Merge branch 'develop' into emerge_gcr_images

  schaluva

  authored
  1d040da

Commits on Sep 22, 2022

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

  Show description for 1ddba6a
  kevinpalis

  authored
  1ddba6a

• Merge branch 'develop' into emerge_gcr_images

  schaluva

  authored
  26853dc

Commits on Sep 26, 2022

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

  timaeusx

  authored
  53f18ad

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

  khajoue2

  authored
  c8f2a9c

Commits on Sep 30, 2022

• Merge branch 'develop' into emerge_gcr_images

  schaluva

  authored
  a876f97

• update arrays changelog

  schaluva

  committed
  cc4f741

• arrays changelogs updated with gcr image

  schaluva

  committed
  cd0eb6e

• update changelogs

  schaluva

  committed
  bc3b8a3

• Merge pull request #828 from broadinstitute/emerge_gcr_images

  Show description for 70317fc
  schaluva

  authored
  70317fc