Code

Azurized wdls#1239

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nikellepetrillo merged 211 commits intodevelopbroadinstitute/warp:developfrom azurized_wdlsbroadinstitute/warp:azurized_wdlsCopy head branch name to clipboardJul 16, 2024

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Commits

Commits on Mar 1, 2024

• small change

  nikellepetrillo

  committed
  445995a

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Commits on Mar 6, 2024

• azurize optimus (#1228)

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  3 peopleauthored
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Commits on Mar 14, 2024

• Ph pd 2514 multiome on terra (#1237)

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  nikellepetrillo

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  phendriksen100

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  76762df

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• Merge branch 'develop' into azurized_wdls

  nikellepetrillo

  authored
  1f9c6e9

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• lost the docker_path in joinmultiomebarcode task

  nikellepetrillo

  committed
  a859091

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• update TestMultiome.wdl

  nikellepetrillo

  committed
  831e244

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• update cutadapt wdl

  nikellepetrillo

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  53c7c27

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• update cutadapt wdl

  nikellepetrillo

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Commits on Mar 15, 2024

• try to fix changelog

  nikellepetrillo

  committed
  f3b0294

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• try to fix changelog

  nikellepetrillo

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• remove cloud provider

  nikellepetrillo

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  e4fcd99

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Commits on Mar 18, 2024

• try adding sas token to azure public bucket

  nikellepetrillo

  committed
  f3b97c8

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• try adding sas token to azure public bucket

  nikellepetrillo

  committed
  c5f2af5

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• try files not strings

  nikellepetrillo

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  c5f462a

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• try files not strings

  nikellepetrillo

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Commits on Mar 19, 2024

• remove cromwell root

  nikellepetrillo

  committed
  11835dd

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• update docs

  kayleemathews

  committed
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• quote whitelist

  nikellepetrillo

  committed
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• Merge remote-tracking branch 'origin/azurized_wdls' into azurized_wdls

  nikellepetrillo

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  d204968

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• quote whitelist

  nikellepetrillo

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• dirs

  nikellepetrillo

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• dirs

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• dirs

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Commits on Mar 20, 2024

• add quotes to whitelist

  nikellepetrillo

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Commits on Mar 21, 2024

• mkdir cromwell_root

  nikellepetrillo

  committed
  208d14b

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• try vm family

  nikellepetrillo

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  cb9bbdb

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• try vm family

  nikellepetrillo

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• Standard_M128s

  nikellepetrillo

  committed
  252bec6

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Commits on Mar 27, 2024

• try not to use cromwell root

  nikellepetrillo

  committed
  5b6d3d3

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• try not to use cromwell root

  nikellepetrillo

  committed
  4024e61

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• try using logic

  nikellepetrillo

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Commits on Mar 28, 2024

• try using logic

  nikellepetrillo

  committed
  32a83fc

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• update snapatac2 docker

  nikellepetrillo

  committed
  4b7a903

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• remove mkdir cromwell root

  nikellepetrillo

  committed
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Commits on Mar 29, 2024

• snap dpcker

  nikellepetrillo

  committed
  d826b0a

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• fix snap dpcker

  nikellepetrillo

  committed
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Commits on Apr 2, 2024

• fix starsolo fastq for other flavors of optimus

  nikellepetrillo

  committed
  9012509

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• merge conflicts

  nikellepetrillo

  committed
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• merge conflicts

  nikellepetrillo

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• merge conflicts

  nikellepetrillo

  committed
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• merge conflicts

  nikellepetrillo

  committed
  ab64432

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Commits on Apr 3, 2024

• fix StarAlign.wdl

  nikellepetrillo

  committed
  537f330

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• put whitelists in quotes

  nikellepetrillo

  committed
  1a0a340

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Commits on Apr 8, 2024

• Merge branch 'develop' into azurized_wdls

  nikellepetrillo

  authored
  30294d0

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• PD-2516: Update Paired-Tag to run in Azure and GCP (#1212)

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  sahakiann

  and

  nikellepetrillo

  authored
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Commits on Apr 11, 2024

• Fk pd 2513 reblock gvcf (#1261)

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  khajoue2

  and

  nikellepetrillo

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Commits on Apr 18, 2024

• edited wdl and changelog for ToA support

  John-Scira

  committed
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• added cloud provider input to test inputs json

  John-Scira

  committed
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• added util class to log error if unsupported cloud provider used for cloud_provider input

  John-Scira

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• added cloud provider parameter to test json

  John-Scira

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  1f6559b

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• refactored task inputs

  John-Scira

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• change to inputs

  John-Scira

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• change to docker path generation

  John-Scira

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• changes made to test wdl

  John-Scira

  committed
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Commits on Apr 19, 2024

• updated reference to docker images for consistency with other azurized wdls

  John-Scira

  committed
  0f6ce91

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• fix to docker image reference

  John-Scira

  committed
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• fix to docker prefix call

  John-Scira

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Commits on Apr 22, 2024

• updated var name

  John-Scira

  committed
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• Merge pull request #1267 from broadinstitute/js_pd-2594_snm3c_runs_on_ToA

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Commits on Apr 29, 2024

• replace hard-coded cromwell_root with variable based on cloud env

  sahakiann

  committed
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• wrap param name in quotations

  sahakiann

  committed
  be70022

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• provide absolute path

  sahakiann

  committed
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• write out files using ls

  sahakiann

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Commits on May 1, 2024

• add print for working dir

  sahakiann

  committed
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• provide absolute paths for demultiplexing

  sahakiann

  committed
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Commits on May 2, 2024

• testing

  sahakiann

  committed
  49b84a3

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• more testing

  sahakiann

  committed
  0f8c6e3

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• more testing

  sahakiann

  committed
  7eca252

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• put things back

  sahakiann

  committed
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Commits on May 3, 2024

• add lots more logging

  sahakiann

  committed
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• only run cutadapt

  sahakiann

  committed
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• only run cutadapt

  sahakiann

  committed
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Commits on May 6, 2024

• write files to current working dir

  sahakiann

  committed
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• write files to current working dir

  sahakiann

  committed
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• write files to current working dir

  sahakiann

  committed
  19a9556

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• add some of demultiplexing steps back in

  sahakiann

  committed
  0605e65

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• typo

  sahakiann

  committed
  e2f98c8

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• typo

  sahakiann

  committed
  1d8745c

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• typo

  sahakiann

  committed
  e672e3d

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• remove print

  sahakiann

  committed
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• uncomment rest of workflow

  sahakiann

  committed
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Commits on May 7, 2024

• add working dir to batch subdir

  sahakiann

  committed
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• ls cromwell root batch

  sahakiann

  committed
  2098784

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• Merge branch 'develop' into azurized_wdls

  nikellepetrillo

  authored
  e57d723

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• ls directories to find batch dir

  sahakiann

  committed
  7704e7d

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• update changelogs

  nikellepetrillo

  committed
  63466c5

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• set batch dir

  sahakiann

  committed
  5ba8021

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• remove extra leading slash

  sahakiann

  committed
  988a920

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Commits on May 8, 2024

• fixing what i messed up in resvoling conflicts

  nikellepetrillo

  committed
  03f5870

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• fix batch dir

  sahakiann

  committed
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Commits on May 9, 2024

• need to loop through array

  nikellepetrillo

  committed
  e63ff3d

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• add lots of logging to batch logic

  sahakiann

  committed
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• add lots of logging to batch logic

  sahakiann

  committed
  9823190

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• change output dir of bams

  sahakiann

  committed
  76ef8e5

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• fix path of fastq

  sahakiann

  committed
  7c28296

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• fix path of fastq

  sahakiann

  committed
  cf24367

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• fix fastq remove path

  sahakiann

  committed
  4d0f214

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• add more echo statements

  sahakiann

  committed
  63ea99a

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• add more echo statements again

  sahakiann

  committed
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• trigger update of wdl in workpace

  sahakiann

  committed
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• remove some logging

  sahakiann

  committed
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Commits on May 10, 2024

• fix logging error syntax

  sahakiann

  committed
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• add missing quote

  sahakiann

  committed
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• Merge branch 'develop' into azurized_wdls

  nikellepetrillo

  authored
  84bb3ec

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• change working dir to batch dir

  sahakiann

  committed
  e0f4863

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• add ls

  nikellepetrillo

  committed
  15269a1

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• version change

  John-Scira

  committed
  2d4626e

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• fix paths

  sahakiann

  committed
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• fix batch dir

  sahakiann

  committed
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• fix batch dir

  sahakiann

  committed
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• fix directories

  sahakiann

  committed
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Commits on May 13, 2024

• moving around inputs

  nikellepetrillo

  committed
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• remove working dir from name of tar file

  nikellepetrillo

  committed
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• take basenames

  nikellepetrillo

  committed
  91b4b7c

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• recursively ls the root to find the batch dirs

  sahakiann

  committed
  60274b9

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• add echo statement

  nikellepetrillo

  committed
  5d2c646

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• added docker parameter for DragenTasks.CalibrateDragstrModel supporting azure

  John-Scira

  committed
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• added docker parameter for Utils.ScatterIntervalList to support azure

  John-Scira

  committed
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• added docker parameter for Calling.HaplotypeCaller_GATK4_VCF to support azure

  John-Scira

  committed
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• added docker parameter for Calling.HaplotypeCaller_GATK4_VCF to support azure

  John-Scira

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• added docker parameter to support azure

  John-Scira

  committed
  3e350bd

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• add echo statement

  nikellepetrillo

  committed
  ee11495

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• fix batch dir

  sahakiann

  committed
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• fix batch dir

  sahakiann

  committed
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• fix path to hisat index files

  sahakiann

  committed
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Commits on May 14, 2024

• add pipline_inputs subdir to location of index files

  sahakiann

  committed
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• add pipline_inputs subdir to location of index files again

  sahakiann

  committed
  352c7af

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• fix tar command

  sahakiann

  committed
  797ba49

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• some clean up, remove pipeline inputs subdir, edit single end task

  sahakiann

  committed
  a1a952b

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• copy fa file again

  sahakiann

  committed
  5162ae4

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• rename some inputs for paired tag demultiplexing

  nikellepetrillo

  committed
  33b28b7

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• Merge remote-tracking branch 'origin/azurized_wdls' into azurized_wdls

  nikellepetrillo

  committed
  2d33803

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• rename some intermediate inputs for paired tag demultiplexing

  nikellepetrillo

  committed
  c0dd626

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• list cromwell root

  sahakiann

  committed
  a2ebd1b

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• fix batch dir

  sahakiann

  committed
  9704a24

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• add conditional for input and output bams

  sahakiann

  committed
  aff8a9c

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• fix logic for cloud provider vs. crowell root dir

  sahakiann

  committed
  f5ef9ad

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• add ls

  sahakiann

  committed
  e12283a

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• fix batch dir in gcp

  sahakiann

  committed
  c6a1216

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• fix sytaxt error

  sahakiann

  committed
  1063475

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• ugh remove echo statements referencing variable that doesnt exist anymore

  sahakiann

  committed
  fefba08

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• attempt to fix syntax error

  sahakiann

  committed
  30a6b93

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• add missing forward slash

  sahakiann

  committed
  ebb3c39

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Commits on May 15, 2024

• fix directories, add ls commands

  sahakiann

  committed
  36a2ce9

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• add more ls commands

  sahakiann

  committed
  18ad64c

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• add more ls commands

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  cd4f876

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• add more ls commands again

  sahakiann

  committed
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• Merge branch 'develop' into azurized_wdls

  sahakiann

  authored
  fe5337b

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• fix fasta file path

  sahakiann

  committed
  2c6d56b

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• changing docker inputs to allow for tests to pass against pipelines that have not yet been azurized

  John-Scira

  committed
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• add more logging, put in cromwell root for move rather than local dir

  sahakiann

  committed
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Commits on May 16, 2024

• fix to docker task inputs to allow default values

  John-Scira

  committed
  2c3a6c5

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• add more logging, add more ls, try tarring files in current dir rather than previous subdir

  sahakiann

  committed
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• use correct syntax for verbose untarring

  sahakiann

  committed
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• fix to docker version

  John-Scira

  committed
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• set correct base dirs that are nested

  sahakiann

  committed
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Commits on May 17, 2024

• change to how cromwell root dir is set

  John-Scira

  committed
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• correction to docker image being used

  John-Scira

  committed
  5d6aaf4

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• add debugging

  sahakiann

  committed
  2fe6f92

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• formatting fix

  John-Scira

  committed
  ff3e6b2

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• add logic for base directory based on gcp vs azure

  sahakiann

  committed
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Commits on May 20, 2024

• added notes to affected changelogs

  John-Scira

  committed
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Commits on May 21, 2024

• updated changelog for WGS Single sample pipeline

  John-Scira

  committed
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• updated pipeline version to match changelong

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• updated pipeline version to match changelong

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• updated pipeline version to match changelong

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• updated changelog and pipeline version

  John-Scira

  committed
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• updated changelog and pipeline version

  John-Scira

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• updated changelog and pipeline version

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• updated changelog and pipeline version

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Commits on May 22, 2024

• Merge branch 'azurized_wdls' into js-pd-2625_variant_calling_azure_support

  John-Scira

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Commits on May 23, 2024

• reverting snm3c changes

  John-Scira

  committed
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• added notes for SlideSeq and changelog for updated tasks

  John-Scira

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Commits on May 24, 2024

• Merge pull request #1277 from broadinstitute/js-pd-2625_variant_calling_azure_support

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Commits on May 29, 2024

• remove logging and debugging statements

  sahakiann

  committed
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• Merge remote-tracking branch 'origin/develop' into develop

  nikellepetrillo

  committed
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Commits on Jun 6, 2024

• Merge remote-tracking branch 'origin/develop' into develop

  nikellepetrillo

  committed
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• conflicts

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Commits on Jun 7, 2024

• just testing

  nikellepetrillo

  committed
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• add input to test

  nikellepetrillo

  committed
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• changelogs

  nikellepetrillo

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• changelogs

  nikellepetrillo

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• Np make vm size an input to multiome (#1289)

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• more disk and mem

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• Azurize Cell Bender in Multiome (#1299)

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• update docker for Summary_PerCellOutput

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• update dockers

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• more changelogs ugh

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• made minor updates, not patches

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• pointing to pinned version of dockers or the sha

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• Apply suggestions from code review

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• doc reformatting

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• Update pipelines/broad/arrays/imputation/Imputation.changelog.md

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• Update pipelines/skylab/slideseq/SlideSeq.changelog.md

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