cromwell

Discussion List

• GATK-Mutect2 Running and Output Error in Terra

  Answered 33 views 1 comment 0 points Most recent by bhanuGandham October 2019Ask the GATK team
• Blue skies ahead for Cromwell on Azure

  107 views 0 comments 0 points Started by Ruchi October 2019 Cromwell + WDL Announcements
• Disadvantages of directly using google genomics pipeline API

  81 views 2 comments 0 points Most recent by taliraveh August 2019Ask the GATK team
• CWL issues with Cromwell 44 (imports and type)

  Question 23 views 0 comments 0 points Started by garyluu August 2019 Ask the Cromwell + WDL Team
• Five dollar pipeline returning error 247

  Question 60 views 0 comments 0 points Started by OggieM July 2019 Ask the Cromwell + WDL Team
• WDL + Cromwell + AWS Batch

  Question 110 views 0 comments 0 points Started by golharam June 2019 Ask the Cromwell + WDL Team
• Variables in task output

  Answered 32 views 1 comment 0 points Most recent by golharam June 2019Ask the Cromwell + WDL Team
• Is the as_map function supported?

  Question 17 views 0 comments 0 points Started by dt7 June 2019 Ask the Cromwell + WDL Team
• Cromwell is slow to submit jobs in large scatter on JES

  Answered 173 views 3 comments 0 points Most recent by erdanieee May 2019Ask the Cromwell + WDL Team
• Pre-data processing pipeline keep copying ubam and reference files for each task

  Answered 45 views 3 comments 0 points Most recent by minimax May 2019Ask the GATK team
• Cromwell notification?

  Answered 62 views 3 comments 0 points Most recent by nrynnv May 2019Ask the Cromwell + WDL Team
• Any utility to convert Python Based tools to WDL

  Question 36 views 0 comments 0 points Started by vinay_is May 2019 Ask the Cromwell + WDL Team
• What (databases, versions) are supported for call caching?

  Question 45 views 0 comments 0 points Started by mmah April 2019 Ask the Cromwell + WDL Team
• Failure while processing large unmapped bam file as input to cromwell

  Answered 60 views 3 comments 0 points Most recent by AdelaideR April 2019Ask the FireCloud Team
• Example from video (AWS Batch + GATK WDL/Cromwell) does not work for me

  Answered 345 views 6 comments 0 points Most recent by aeahmed April 2019Ask the Cromwell + WDL Team
• Can AWS Key:Value tags be passed through wdl to cromwell?

  Answered 27 views 3 comments 0 points Most recent by aeahmed April 2019Ask the Cromwell + WDL Team
• Done in the VM, but no output on firecloud

  Accepted Answer 26 views 4 comments 0 points Most recent by cbao March 2019Ask the FireCloud Team
• Cromwell hangs at "Starting" execution status when using select_first on an optional Array

  Answered 63 views 1 comment 0 points Most recent by markw March 2019Ask the Cromwell + WDL Team
• GATK on Amazon Web Services

  341 views 1 comment 0 points Most recent by gunns March 2019Computing Platforms
• Long directory paths cause jobs to fail

  Answered 22 views 1 comment 0 points Most recent by matdmset March 2019Ask the Cromwell + WDL Team
• 热烈欢迎我们的中国朋友 / A warm welcome to our Chinese friends

  534 views 11 comments 2 points Most recent by liuym March 2019Announcements
• Output of workflows not overwriting values in the sample entity

  Answered 41 views 1 comment 0 points Most recent by SChaluvadi March 2019Ask the FireCloud Team
• Scatter:Gather by array indices

  Accepted Answer 97 views 3 comments 0 points Most recent by ChrisL February 2019Ask the Cromwell + WDL Team
• Question about read_object function usage

  Question 10 views 1 comment 0 points Most recent by blawney February 2019Ask the Cromwell + WDL Team
• Somatic mutation pipeline error at"WorkflowManagerActor Workflow 709e5b32-05c0-4e49-96b7-bc5c4ab56"

  Answered 103 views 2 comments 0 points Most recent by suimye February 2019Ask the GATK team
• Cromwell terminates unexpectedly in Google cloud. UnknownHostException: genomics.googleapis.com

  Answered 118 views 5 comments 0 points Most recent by GrantDaly February 2019Ask the Cromwell + WDL Team
• Submit entire workflow to SLURM instead of individual tasks

  Question 81 views 0 comments 0 points Started by Dorjee February 2019 Ask the Cromwell + WDL Team
• AWS and GCP error parsing WDL with "Unrecognized token"

  Accepted Answer 71 views 1 comment 0 points Most recent by deconti January 2019Ask the Cromwell + WDL Team
• issues submitting with the 'submit' subcommand of the cromwell jar file

  Answered 126 views 2 comments 0 points Most recent by dtenenba January 2019Ask the Cromwell + WDL Team
• 1

  Up
  Specifying Intermediate Files

  Active 88 views 4 comments 1 point Most recent by gkugener January 2019Feature Requests
• Working with Requester Pays S3 buckets

  Accepted Answer 114 views 0 comments 0 points Started by dtenenba January 2019 Ask the Cromwell + WDL Team
• CWL workflow fails running locally

  Accepted Answer 153 views 0 comments 0 points Started by dtenenba December 2018 Ask the Cromwell + WDL Team
• Calling sub() on a (localized) File

  Accepted Answer 56 views 2 comments 0 points Most recent by ChrisL December 2018Ask the Cromwell + WDL Team
• AWS Batch - how to use pre-existing job definition or specify docker container

  Answered 156 views 7 comments 0 points Most recent by wleepang November 2018Ask the Cromwell + WDL Team
• S3 Example fails

  Accepted Answer 119 views 1 comment 0 points Most recent by dtenenba November 2018Ask the Cromwell + WDL Team
• running cromwell with google cloud call VM with external IP address

  Accepted Answer 223 views 9 comments 0 points Most recent by SChaluvadi November 2018Ask the FireCloud Team
• java.sql.SQLNonTransientConnectionException after finishing workflow

  Accepted Answer 1K views 5 comments 0 points Most recent by dbecker November 2018Ask the FireCloud Team
• Tasks queued in Cromwell

  Accepted Answer 108 views 11 comments 0 points Most recent by SChaluvadi November 2018Ask the FireCloud Team
• workflow: SingleWorkflowRunnerActor workflow finished with status 'Failed'.

  Accepted Answer 514 views 9 comments 0 points Most recent by SChaluvadi November 2018Ask the FireCloud Team
• Unable to launch jobs

  Accepted Answer 20 views 2 comments 0 points Most recent by SChaluvadi November 2018Ask the FireCloud Team
• Is this error caused by a job submission failure?

  Accepted Answer 691 views 14 comments 1 point Most recent by alongalor November 2018Ask the Cromwell + WDL Team
• Will the Cromwell upgrade on 11/1/2018 2:30 - 3:30 pm EST kill jobs?

  Accepted Answer 26 views 2 comments 0 points Most recent by breardon November 2018Ask the FireCloud Team
• New CloudSQL database fails initial migration

  Accepted Answer 83 views 1 comment 0 points Most recent by danb October 2018Ask the Cromwell + WDL Team
• Cromwell + Google Cloud MySQL

  Accepted Answer 101 views 1 comment 0 points Most recent by mooses October 2018Ask the Cromwell + WDL Team
• How are files and auto-scaling supposed to work on AWS?

  Accepted Answer 77 views 0 comments 0 points Started by seandavi October 2018 Ask the Cromwell + WDL Team
• Running Cromwell on AWS Batch, using both S3 and GC filesystems

  Accepted Answer 248 views 0 comments 0 points Started by Migwell October 2018 Ask the Cromwell + WDL Team
• cnv_somatic_panel_workflow.wdl: Status change from - to WaitingForReturnCodeFile is hanging

  Accepted Answer 207 views 10 comments 0 points Most recent by fholst October 2018Ask the Cromwell + WDL Team
• Multiple issues with FC workflow execution & call caching

  Accepted Answer 99 views 6 comments 0 points Most recent by RLCollins October 2018Ask the FireCloud Team
• Cromwell 35 expands support to AWS Batch and upgrades GCP backend to PAPI v2

  185 views 0 comments 0 points Started by Ruchi October 2018 Cromwell + WDL Announcements
• Cromwell runtime 'memory' units

  Accepted Answer 125 views 1 comment 0 points Most recent by Ruchi September 2018Ask the Cromwell + WDL Team
• Possible to distribute work across multiple types of environment

  Answered 47 views 3 comments 0 points Most recent by Ruchi August 2018Ask the Cromwell + WDL Team
• Cromwell configuration on SLURM

  Accepted Answer 315 views 2 comments 0 points Most recent by grace_G August 2018Ask the Cromwell + WDL Team
• The job was aborted from outside Cromwell: How to get around this error?

  Accepted Answer 118 views 5 comments 0 points Most recent by DivyKangeyan August 2018Ask the FireCloud Team
• How to specify an output directory by the cromwell option or in the json input file?

  Answered 692 views 1 comment 0 points Most recent by Ruchi August 2018Ask the Cromwell + WDL Team
• Slowdown & 15m periodicity when checking call cache

  Accepted Answer 88 views 3 comments 0 points Most recent by RLCollins August 2018Ask the FireCloud Team
• Why is Cromwell launching "n1-ultramem-40" GCE instance when I ask for 'memory: "16 GB" cpu: 36'?

  Accepted Answer 106 views 1 comment 0 points Most recent by ChrisL August 2018Ask the Cromwell + WDL Team
• five-dollar-genome-analysis-pipeline running errors in CheckContamination

  Answered 126 views 4 comments 0 points Most recent by ebanks August 2018Ask the FireCloud Team
• Tabix-incompatible file creation times

  Accepted Answer 95 views 5 comments 0 points Most recent by KateN July 2018Ask the FireCloud Team
• Option for less verbose Cromwell stdout?

  Answered 48 views 1 comment 0 points Most recent by jgentry July 2018Ask the Cromwell + WDL Team
• [WDL][Cromwell[ Mounting a directory to the docker for access.

  Accepted Answer 923 views 13 comments 0 points Most recent by Sheila July 2018Ask the GATK team
• long wait time between workflow finishing and getting final workflow status

  Answered 103 views 2 comments 0 points Most recent by ChrisL June 2018Ask the Cromwell + WDL Team
• Why does this work?

  Answered 94 views 4 comments 0 points Most recent by ChrisL June 2018Ask the Cromwell + WDL Team
• Can Cromwell limit the number of concurrent jobs for a particular task?

  Accepted Answer 180 views 1 comment 0 points Most recent by Thib June 2018Ask the Cromwell + WDL Team
• not-working mutect2 WDL pipeline.

  Answered 133 views 1 comment 1 point Most recent by Sheila June 2018Ask the GATK team
• Can I query by multiple labels using json POST?

  Accepted Answer 38 views 0 comments 0 points Started by lkajan May 2018 Ask the Cromwell + WDL Team
• You can't spell Cromwell without CWL

  349 views 0 comments 0 points Started by jgentry May 2018 Cromwell + WDL Announcements
• When Are Cromwell Timing Graphs Generated?

  Accepted Answer 86 views 1 comment 0 points Most recent by Thib May 2018Ask the Cromwell + WDL Team
• Call QueuedInCromwell, Job Running?

  Accepted Answer 283 views 14 comments 0 points Most recent by Geraldine_VdAuwera May 2018Ask the FireCloud Team
• How to localise a directory with a symbolic link using Cromwell?

  Accepted Answer 187 views 0 comments 0 points Started by santiagorevale May 2018 Ask the Cromwell + WDL Team
• Pre-start hook?

  Answered 136 views 2 comments 0 points Most recent by edpark_clearlabs May 2018Ask the Cromwell + WDL Team
• Building cromwell 31

  Accepted Answer 105 views 9 comments 0 points Most recent by danb May 2018Ask the Cromwell + WDL Team
• Is the a dev guide to writing cromwell backends?

  Accepted Answer 74 views 2 comments 0 points Most recent by mathias1 May 2018Ask the Cromwell + WDL Team
• How do I cite tools such as firecloud, WDL and cromwell?

  Accepted Answer 176 views 2 comments 0 points Most recent by DivyKangeyan May 2018Ask the FireCloud Team
• Running Cromwell

  Accepted Answer 128 views 0 comments 0 points Started by afrieden April 2018 Ask the Cromwell + WDL Team
• ImportGVCFs error message "Failed to create reader from file"

  Accepted Answer 1.3K views 2 comments 0 points Most recent by bshifaw April 2018Ask the GATK team
• Bug: Queued in Cromwell

  Accepted Answer 153 views 4 comments 0 points Most recent by mcovarr April 2018Ask the FireCloud Team
• extraneous copies of input files

  Answered 90 views 4 comments 0 points Most recent by Thib March 2018Ask the Cromwell + WDL Team
• Deleting intermediate files

  Answered 789 views 12 comments 0 points Most recent by dinvlad March 2018Ask the Cromwell + WDL Team
• getting tail of the array

  Answered 180 views 4 comments 0 points Most recent by ChrisL March 2018Ask the Cromwell + WDL Team
• Multiple workflow languages coming to Cromwell, starting with CWL

  871 views 3 comments 0 points Most recent by jgentry February 2018Cromwell + WDL Announcements
• Array input in a json file for cromwell

  Accepted Answer 675 views 3 comments 0 points Most recent by DivyKangeyan February 2018Ask the Cromwell + WDL Team
• Any way to set concurrent-job-limit dynamically?

  Accepted Answer 170 views 4 comments 0 points Most recent by Thib February 2018Ask the Cromwell + WDL Team
• How much memory does Cromwell need for input or output files?

  Accepted Answer 434 views 4 comments 0 points Most recent by kshakir February 2018Ask the Cromwell + WDL Team
• Cromwell call-caching Failed to hash error

  Answered 78 views 1 comment 0 points Most recent by kshakir February 2018Ask the Cromwell + WDL Team
• Problem with running gatk haplotypecaller in cromwell with spark backend

  Answered 465 views 1 comment 0 points Most recent by henderj8 February 2018Ask the Cromwell + WDL Team
• How to import workflows that also have imports themselves?

  Answered 407 views 5 comments 0 points Most recent by rhpvorderman February 2018Ask the Cromwell + WDL Team
• Cromwell call-caching Failed to hash error

  Answered 139 views 4 comments 0 points Most recent by jsoto January 2018Ask the Cromwell + WDL Team
• GATK on the cloud with Terra (previously FireCloud)

  230 views 0 comments 0 points Started by Geraldine_VdAuwera January 2018 Computing Platforms
• GATK on BIGstack for local HPC infrastructure

  250 views 0 comments 0 points Started by GATK_Team January 2018 Computing Platforms
• GATK on Alibaba Cloud

  168 views 0 comments 0 points Started by Geraldine_VdAuwera January 2018 Computing Platforms
• GATK on Google Cloud

  710 views 0 comments 0 points Started by Geraldine_VdAuwera January 2018 Computing Platforms
• Pipelining GATK with WDL and Cromwell

  563 views 0 comments 0 points Started by GATK_Team January 2018 Computing Platforms
• Parallelism - Multithreading - Scatter Gather

  1.2K views 0 comments 2 points Started by GATK_Team December 2017 Dictionary
• Cromwell

  119 views 0 comments 0 points Started by Tiffany_at_Broad December 2017 Dictionary
• Where can I get help with WDL and Cromwell?

  156 views 0 comments 0 points Started by KateN December 2017 Frequently Asked Questions
• How to delocalize a file whose name is in a file?

  Accepted Answer 251 views 3 comments 1 point Most recent by ChrisL December 2017Ask the Cromwell + WDL Team
• Any way (or plan) ro launch WDL in FireCloud without creating workspace?

  Answered 92 views 1 comment 0 points Most recent by KateN December 2017Ask the FireCloud Team
• [ERROR] the local copy message must have path set.

  Accepted Answer 170 views 7 comments 0 points Most recent by cbao November 2017Ask the FireCloud Team
• String substitution over-quotes string in output section when default value is used

  Accepted Answer 126 views 1 comment 0 points Most recent by dpark November 2017Ask the Cromwell + WDL Team
• String? type in output section

  Accepted Answer 174 views 3 comments 0 points Most recent by ChrisL October 2017Ask the Cromwell + WDL Team