cromwell

Discussion List

• Running Cromwell on AWS Batch, using both S3 and GC filesystems

  Question 2 views 0 comments 0 points Started by Migwell October 15 Ask the Cromwell + WDL Team
• cnv_somatic_panel_workflow.wdl: Status change from - to WaitingForReturnCodeFile is hanging

  Question 51 views 10 comments 0 points Most recent by fholst October 9Ask the Cromwell + WDL Team
• java.sql.SQLNonTransientConnectionException after finishing workflow

  Question 13 views 0 comments 0 points Started by dbecker October 8 Ask the GATK team
• Multiple issues with FC workflow execution & call caching

  Answered 69 views 6 comments 0 points Most recent by RLCollins October 4Ask the FireCloud Team
• workflow: SingleWorkflowRunnerActor workflow finished with status 'Failed'.

  Accepted Answer 53 views 6 comments 0 points Most recent by KateN October 3Ask the FireCloud Team
• Cromwell 35 expands support to AWS Batch and upgrades GCP backend to PAPI v2

  24 views 0 comments 0 points Started by Ruchi October 1 Cromwell + WDL Announcements
• Cromwell runtime 'memory' units

  Accepted Answer 30 views 1 comment 0 points Most recent by Ruchi September 6Ask the Cromwell + WDL Team
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  Specifying Intermediate Files

  Active 12 views 0 comments 1 point Started by qwessell September 5 Feature Requests
• Cromwell is slow to submit jobs in large scatter on JES

  Answered 48 views 2 comments 0 points Most recent by jweinstk September 2Ask the Cromwell + WDL Team
• Possible to distribute work across multiple types of environment

  Answered 14 views 3 comments 0 points Most recent by Ruchi August 31Ask the Cromwell + WDL Team
• Cromwell configuration on SLURM

  Accepted Answer 50 views 2 comments 0 points Most recent by grace_G August 29Ask the Cromwell + WDL Team
• Is this error caused by a job submission failure?

  Accepted Answer 174 views 13 comments 1 point Most recent by JohnyWalter August 20Ask the Cromwell + WDL Team
• The job was aborted from outside Cromwell: How to get around this error?

  Accepted Answer 51 views 5 comments 0 points Most recent by DivyKangeyan August 10Ask the FireCloud Team
• How to specify an output directory by the cromwell option or in the json input file?

  Answered 33 views 1 comment 0 points Most recent by Ruchi August 8Ask the Cromwell + WDL Team
• Slowdown & 15m periodicity when checking call cache

  Accepted Answer 67 views 3 comments 0 points Most recent by RLCollins August 8Ask the FireCloud Team
• Why is Cromwell launching "n1-ultramem-40" GCE instance when I ask for 'memory: "16 GB" cpu: 36'?

  Accepted Answer 34 views 1 comment 0 points Most recent by ChrisL August 2Ask the Cromwell + WDL Team
• five-dollar-genome-analysis-pipeline running errors in CheckContamination

  Answered 64 views 4 comments 0 points Most recent by ebanks August 1Ask the FireCloud Team
• Tabix-incompatible file creation times

  Accepted Answer 46 views 5 comments 0 points Most recent by KateN July 31Ask the FireCloud Team
• Option for less verbose Cromwell stdout?

  Answered 28 views 1 comment 0 points Most recent by jgentry July 27Ask the Cromwell + WDL Team
• running cromwell with google cloud call VM with external IP address

  Answered 32 views 2 comments 0 points Most recent by Ruchi July 5Ask the GATK team
• [WDL][Cromwell[ Mounting a directory to the docker for access.

  Accepted Answer 475 views 13 comments 0 points Most recent by Sheila July 2Ask the GATK team
• long wait time between workflow finishing and getting final workflow status

  Question 80 views 2 comments 0 points Most recent by ChrisL June 13Ask the Cromwell + WDL Team
• Why does this work?

  Answered 37 views 4 comments 0 points Most recent by ChrisL June 12Ask the Cromwell + WDL Team
• Can Cromwell limit the number of concurrent jobs for a particular task?

  Answered 46 views 1 comment 0 points Most recent by Thib June 2Ask the Cromwell + WDL Team
• not-working mutect2 WDL pipeline.

  Answered 34 views 1 comment 0 points Most recent by Sheila June 1Ask the GATK team
• Can I query by multiple labels using json POST?

  Question 23 views 0 comments 0 points Started by lkajan May 31 Ask the Cromwell + WDL Team
• You can't spell Cromwell without CWL

  91 views 0 comments 0 points Started by jgentry May 25 Cromwell + WDL Announcements
• When Are Cromwell Timing Graphs Generated?

  Accepted Answer 29 views 1 comment 0 points Most recent by Thib May 23Ask the Cromwell + WDL Team
• Call QueuedInCromwell, Job Running?

  Accepted Answer 230 views 14 comments 0 points Most recent by Geraldine_VdAuwera May 19Ask the FireCloud Team
• How to localise a directory with a symbolic link using Cromwell?

  Question 69 views 0 comments 0 points Started by santiagorevale May 18 Ask the Cromwell + WDL Team
• Pre-start hook?

  Answered 35 views 2 comments 0 points Most recent by edpark_clearlabs May 16Ask the Cromwell + WDL Team
• Building cromwell 31

  Accepted Answer 39 views 9 comments 0 points Most recent by danb May 7Ask the Cromwell + WDL Team
• Is the a dev guide to writing cromwell backends?

  Accepted Answer 33 views 2 comments 0 points Most recent by mathias1 May 7Ask the Cromwell + WDL Team
• How do I cite tools such as firecloud, WDL and cromwell?

  Accepted Answer 97 views 2 comments 0 points Most recent by DivyKangeyan May 7Ask the FireCloud Team
• Running Cromwell

  Question 52 views 0 comments 0 points Started by afrieden April 29 Ask the Cromwell + WDL Team
• ImportGVCFs error message "Failed to create reader from file"

  Accepted Answer 308 views 2 comments 0 points Most recent by bshifaw April 17Ask the GATK team
• Bug: Queued in Cromwell

  Accepted Answer 104 views 4 comments 0 points Most recent by mcovarr April 12Ask the FireCloud Team
• extraneous copies of input files

  Answered 51 views 4 comments 0 points Most recent by Thib March 30Ask the Cromwell + WDL Team
• Deleting intermediate files

  Answered 352 views 12 comments 0 points Most recent by dinvlad March 9Ask the Cromwell + WDL Team
• getting tail of the array

  Answered 92 views 4 comments 0 points Most recent by ChrisL March 3Ask the Cromwell + WDL Team
• Multiple workflow languages coming to Cromwell, starting with CWL

  526 views 3 comments 0 points Most recent by jgentry February 28Cromwell + WDL Announcements
• Array input in a json file for cromwell

  Accepted Answer 190 views 3 comments 0 points Most recent by DivyKangeyan February 26Ask the Cromwell + WDL Team
• Any way to set concurrent-job-limit dynamically?

  Accepted Answer 52 views 4 comments 0 points Most recent by Thib February 22Ask the Cromwell + WDL Team
• How much memory does Cromwell need for input or output files?

  Accepted Answer 236 views 4 comments 0 points Most recent by kshakir February 8Ask the Cromwell + WDL Team
• Cromwell call-caching Failed to hash error

  Answered 39 views 1 comment 0 points Most recent by kshakir February 8Ask the Cromwell + WDL Team
• Problem with running gatk haplotypecaller in cromwell with spark backend

  Answered 314 views 1 comment 0 points Most recent by henderj8 February 8Ask the Cromwell + WDL Team
• How to import workflows that also have imports themselves?

  Answered 127 views 5 comments 0 points Most recent by rhpvorderman February 8Ask the Cromwell + WDL Team
• Cromwell call-caching Failed to hash error

  Answered 73 views 4 comments 0 points Most recent by jsoto January 18Ask the Cromwell + WDL Team
• GATK on FireCloud

  122 views 0 comments 0 points Started by Geraldine_VdAuwera January 7 Pipelining Options
• GATK on Intel BIGstack for on-premises infrastructure

  93 views 0 comments 0 points Started by Geraldine_VdAuwera January 7 Pipelining Options
• GATK on Alibaba Cloud

  86 views 0 comments 0 points Started by Geraldine_VdAuwera January 7 Pipelining Options
• GATK on Google Cloud

  209 views 0 comments 0 points Started by Geraldine_VdAuwera January 7 Pipelining Options
• GATK on Amazon Web Services

  174 views 0 comments 0 points Started by Geraldine_VdAuwera January 7 Pipelining Options
• Pipelining recommendations

  234 views 0 comments 0 points Started by GATK_Team January 7 Pipelining Options
• Parallelism - Multithreading - Scatter Gather

  344 views 0 comments 1 point Started by GATK_Team December 2017 Dictionary
• Cromwell

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

  116 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 84 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 76 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 112 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 44 views 1 comment 0 points Most recent by dpark November 2017Ask the Cromwell + WDL Team
• String? type in output section

  Accepted Answer 53 views 3 comments 0 points Most recent by ChrisL October 2017Ask the Cromwell + WDL Team
• connection reset by peer, defining memory is not working

  Answered 133 views 5 comments 0 points Most recent by shlee October 2017Ask the Cromwell + WDL Team
• 热烈欢迎我们的中国朋友 / A warm welcome to our Chinese friends

  416 views 10 comments 2 points Most recent by cbao September 2017Announcements
• Localization via hard link has failed

  Answered 189 views 11 comments 0 points Most recent by kshakir September 2017Ask the Cromwell + WDL Team
• Bug: Cromwell removes empty spaces from WDL when creating exec.sh

  Accepted Answer 61 views 3 comments 0 points Most recent by Tiffany_at_Broad September 2017Ask the Cromwell + WDL Team
• String expanding to array after scatter block

  Accepted Answer 29 views 1 comment 0 points Most recent by ChrisL September 2017Ask the Cromwell + WDL Team
• color in the output to screen from cromwell run

  Accepted Answer 137 views 20 comments 0 points Most recent by blueskypy September 2017Ask the Cromwell + WDL Team
• Using Docker Content Trust with Cromwell

  Answered 133 views 6 comments 0 points Most recent by mcovarr September 2017Ask the Cromwell + WDL Team
• Is it possible that WDLTool accepts filenames that start with numbers and contain underscores?

  Accepted Answer 49 views 2 comments 0 points Most recent by Yatros September 2017Ask the Cromwell + WDL Team
• Easy fix in the documentation in hte Running section

  Accepted Answer 42 views 1 comment 0 points Most recent by Geraldine_VdAuwera August 2017Ask the Cromwell + WDL Team
• Retrieving metadata for large workflows

  Accepted Answer 76 views 6 comments 0 points Most recent by mcovarr August 2017Ask the Cromwell + WDL Team
• Cromwell workflows appear hung

  Accepted Answer 144 views 11 comments 0 points Most recent by mcovarr August 2017Ask the Cromwell + WDL Team
• Feature Request: Add username to database

  Accepted Answer 66 views 13 comments 0 points Most recent by Ruchi August 2017Ask the Cromwell + WDL Team
• How to know which job failed in continuewhenpossible mode?

  Answered 63 views 3 comments 0 points Most recent by ChrisL August 2017Ask the Cromwell + WDL Team
• WDL fail with NoSuchFileException, but the file exists

  Accepted Answer 298 views 12 comments 0 points Most recent by awacs August 2017Ask the Cromwell + WDL Team
• Scatter Gather and Spark together

  Accepted Answer 287 views 2 comments 1 point Most recent by Geraldine_VdAuwera August 2017Ask the Cromwell + WDL Team
• Syntax change in Cromwell v29 command line

  32 views 0 comments 0 points Started by Geraldine_VdAuwera August 2017 Cromwell + WDL Announcements
• [cromwell 28_2] MySQL database issue: Specified key was too long; max key length is 1000 bytes

  Accepted Answer 224 views 10 comments 0 points Most recent by ChrisL August 2017Ask the Cromwell + WDL Team
• Best practices for large scatter operations

  Answered 148 views 4 comments 0 points Most recent by ChrisL August 2017Ask the Cromwell + WDL Team
• Reduce verbosity of cromwell run

  Accepted Answer 93 views 2 comments 0 points Most recent by Ruchi August 2017Ask the Cromwell + WDL Team
• runnig wdl workflow with cromwell on google cloud

  Answered 245 views 5 comments 0 points Most recent by idan_g August 2017Ask the Cromwell + WDL Team
• running wdl on google genomics

  Accepted Answer 215 views 6 comments 0 points Most recent by afrieden July 2017Ask the Cromwell + WDL Team
• read_tsv failed because the file was too big

  Answered 62 views 1 comment 0 points Most recent by danb July 2017Ask the Cromwell + WDL Team
• Forcing cromwell to submit all possible jobs at once

  Answered 105 views 1 comment 0 points Most recent by kshakir July 2017Ask the Cromwell + WDL Team
• cromwell on sge with containers

  Answered 98 views 1 comment 0 points Most recent by jgentry July 2017Ask the Cromwell + WDL Team
• cromwell error: failed to find index Success on array

  Accepted Answer 212 views 12 comments 0 points Most recent by jweinstk July 2017Ask the Cromwell + WDL Team
• stopping a pipeline using cromwell API

  Accepted Answer 186 views 11 comments 0 points Most recent by ChrisL July 2017Ask the Cromwell + WDL Team
• Cromwell support for docker with -w option to change current working directory inside container

  Answered 245 views 3 comments 0 points Most recent by ChrisL July 2017Ask the Cromwell + WDL Team
• Logging variable values at each stage of the workflow

  Accepted Answer 67 views 2 comments 0 points Most recent by Migwell June 2017Ask the Cromwell + WDL Team
• MySQL cache migration when updating Cromwell version

  Answered 42 views 5 comments 0 points Most recent by danb June 2017Ask the Cromwell + WDL Team
• Question on caching

  Accepted Answer 62 views 5 comments 0 points Most recent by danb June 2017Ask the Cromwell + WDL Team
• [warn] Localization via hard link has failed Invalid cross-device link

  Answered 383 views 14 comments 0 points Most recent by mcovarr June 2017Ask the Cromwell + WDL Team
• Setting Up a Cromwell VM

  Answered 103 views 5 comments 0 points Most recent by Geraldine_VdAuwera June 2017Ask the Cromwell + WDL Team
• Diagnosing call caching behavior

  Accepted Answer 134 views 5 comments 0 points Most recent by mcovarr June 2017Ask the Cromwell + WDL Team
• Documentation on cromwell database mapping

  Accepted Answer 63 views 1 comment 0 points Most recent by Ruchi June 2017Ask the Cromwell + WDL Team
• Selectively disable call caching?

  Accepted Answer 96 views 1 comment 0 points Most recent by Ruchi June 2017Ask the Cromwell + WDL Team
• How to Query for Custom Labels in Cromwell

  Accepted Answer 116 views 6 comments 0 points Most recent by Ruchi June 2017Ask the Cromwell + WDL Team
• Docker image hashing issues in some scenarios with TES backend

  Answered 73 views 1 comment 0 points Most recent by Ruchi May 2017Ask the Cromwell + WDL Team
• Cromwell won't run, waiting for changelog lock

  Accepted Answer 158 views 1 comment 0 points Most recent by ChrisL May 2017Ask the Cromwell + WDL Team