cromwell

Discussion List

• Calling sub() on a (localized) File

  Accepted Answer 5 views 1 comment 0 points Most recent by dtenenba December 12Ask the Cromwell + WDL Team
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  Specifying Intermediate Files

  Active 24 views 1 comment 1 point Most recent by Ruchi December 6Feature Requests
• Example from video (AWS Batch + GATK WDL/Cromwell) does not work for me

  Answered 51 views 4 comments 0 points Most recent by Ruchi December 3Ask the Cromwell + WDL Team
• AWS Batch - how to use pre-existing job definition or specify docker container

  Answered 22 views 7 comments 0 points Most recent by wleepang November 21Ask the Cromwell + WDL Team
• S3 Example fails

  Accepted Answer 16 views 1 comment 0 points Most recent by dtenenba November 18Ask the Cromwell + WDL Team
• running cromwell with google cloud call VM with external IP address

  Accepted Answer 100 views 9 comments 0 points Most recent by SChaluvadi November 8Ask the FireCloud Team
• java.sql.SQLNonTransientConnectionException after finishing workflow

  Accepted Answer 88 views 5 comments 0 points Most recent by dbecker November 8Ask the FireCloud Team
• Tasks queued in Cromwell

  Accepted Answer 65 views 11 comments 0 points Most recent by SChaluvadi November 7Ask the FireCloud Team
• workflow: SingleWorkflowRunnerActor workflow finished with status 'Failed'.

  Accepted Answer 117 views 9 comments 0 points Most recent by SChaluvadi November 2Ask the FireCloud Team
• Unable to launch jobs

  Accepted Answer 14 views 2 comments 0 points Most recent by SChaluvadi November 2Ask the FireCloud Team
• Is this error caused by a job submission failure?

  Accepted Answer 218 views 14 comments 1 point Most recent by alongalor November 1Ask the Cromwell + WDL Team
• Will the Cromwell upgrade on 11/1/2018 2:30 - 3:30 pm EST kill jobs?

  Accepted Answer 13 views 2 comments 0 points Most recent by breardon November 1Ask the FireCloud Team
• New CloudSQL database fails initial migration

  Accepted Answer 4 views 1 comment 0 points Most recent by danb October 31Ask the Cromwell + WDL Team
• Cromwell + Google Cloud MySQL

  Accepted Answer 25 views 1 comment 0 points Most recent by mooses October 26Ask the Cromwell + WDL Team
• How are files and auto-scaling supposed to work on AWS?

  Question 12 views 0 comments 0 points Started by seandavi October 25 Ask the Cromwell + WDL Team
• Running Cromwell on AWS Batch, using both S3 and GC filesystems

  Question 48 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 71 views 10 comments 0 points Most recent by fholst October 9Ask the Cromwell + WDL Team
• Multiple issues with FC workflow execution & call caching

  Accepted Answer 81 views 6 comments 0 points Most recent by RLCollins October 4Ask the FireCloud Team
• Cromwell 35 expands support to AWS Batch and upgrades GCP backend to PAPI v2

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

  Accepted Answer 43 views 1 comment 0 points Most recent by Ruchi September 6Ask the Cromwell + WDL Team
• Cromwell is slow to submit jobs in large scatter on JES

  Answered 59 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 23 views 3 comments 0 points Most recent by Ruchi August 31Ask the Cromwell + WDL Team
• Cromwell configuration on SLURM

  Accepted Answer 85 views 2 comments 0 points Most recent by grace_G August 29Ask the Cromwell + WDL Team
• The job was aborted from outside Cromwell: How to get around this error?

  Accepted Answer 59 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 72 views 1 comment 0 points Most recent by Ruchi August 8Ask the Cromwell + WDL Team
• Slowdown & 15m periodicity when checking call cache

  Accepted Answer 70 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 44 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 77 views 4 comments 0 points Most recent by ebanks August 1Ask the FireCloud Team
• Tabix-incompatible file creation times

  Accepted Answer 50 views 5 comments 0 points Most recent by KateN July 31Ask the FireCloud Team
• Option for less verbose Cromwell stdout?

  Answered 31 views 1 comment 0 points Most recent by jgentry July 27Ask the Cromwell + WDL Team
• [WDL][Cromwell[ Mounting a directory to the docker for access.

  Accepted Answer 535 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 84 views 2 comments 0 points Most recent by ChrisL June 13Ask the Cromwell + WDL Team
• Why does this work?

  Answered 44 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?

  Accepted Answer 59 views 1 comment 0 points Most recent by Thib June 2Ask the Cromwell + WDL Team
• not-working mutect2 WDL pipeline.

  Answered 38 views 1 comment 0 points Most recent by Sheila June 1Ask the GATK team
• Can I query by multiple labels using json POST?

  Question 26 views 0 comments 0 points Started by lkajan May 31 Ask the Cromwell + WDL Team
• You can't spell Cromwell without CWL

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

  Accepted Answer 32 views 1 comment 0 points Most recent by Thib May 23Ask the Cromwell + WDL Team
• Call QueuedInCromwell, Job Running?

  Accepted Answer 238 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 85 views 0 comments 0 points Started by santiagorevale May 18 Ask the Cromwell + WDL Team
• Pre-start hook?

  Answered 40 views 2 comments 0 points Most recent by edpark_clearlabs May 16Ask the Cromwell + WDL Team
• Building cromwell 31

  Accepted Answer 51 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 40 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 110 views 2 comments 0 points Most recent by DivyKangeyan May 7Ask the FireCloud Team
• Running Cromwell

  Question 58 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 484 views 2 comments 0 points Most recent by bshifaw April 17Ask the GATK team
• Bug: Queued in Cromwell

  Accepted Answer 110 views 4 comments 0 points Most recent by mcovarr April 12Ask the FireCloud Team
• extraneous copies of input files

  Answered 59 views 4 comments 0 points Most recent by Thib March 30Ask the Cromwell + WDL Team
• Deleting intermediate files

  Answered 417 views 12 comments 0 points Most recent by dinvlad March 9Ask the Cromwell + WDL Team
• getting tail of the array

  Answered 100 views 4 comments 0 points Most recent by ChrisL March 3Ask the Cromwell + WDL Team
• Multiple workflow languages coming to Cromwell, starting with CWL

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

  Accepted Answer 257 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 68 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 261 views 4 comments 0 points Most recent by kshakir February 8Ask the Cromwell + WDL Team
• Cromwell call-caching Failed to hash error

  Answered 51 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 341 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 179 views 5 comments 0 points Most recent by rhpvorderman February 8Ask the Cromwell + WDL Team
• Cromwell call-caching Failed to hash error

  Answered 82 views 4 comments 0 points Most recent by jsoto January 18Ask the Cromwell + WDL Team
• GATK on FireCloud

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

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

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

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

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

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

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

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

  122 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 102 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 77 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 119 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 53 views 1 comment 0 points Most recent by dpark November 2017Ask the Cromwell + WDL Team
• String? type in output section

  Accepted Answer 59 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 143 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

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

  Answered 240 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 68 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 31 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 156 views 20 comments 0 points Most recent by blueskypy September 2017Ask the Cromwell + WDL Team
• Using Docker Content Trust with Cromwell

  Answered 149 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 51 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 45 views 1 comment 0 points Most recent by Geraldine_VdAuwera August 2017Ask the Cromwell + WDL Team
• Retrieving metadata for large workflows

  Accepted Answer 85 views 6 comments 0 points Most recent by mcovarr August 2017Ask the Cromwell + WDL Team
• Cromwell workflows appear hung

  Accepted Answer 157 views 11 comments 0 points Most recent by mcovarr August 2017Ask the Cromwell + WDL Team
• Feature Request: Add username to database

  Accepted Answer 69 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 71 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 359 views 12 comments 0 points Most recent by awacs August 2017Ask the Cromwell + WDL Team
• Scatter Gather and Spark together

  Accepted Answer 318 views 2 comments 1 point Most recent by Geraldine_VdAuwera August 2017Ask the Cromwell + WDL Team
• Syntax change in Cromwell v29 command line

  38 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 265 views 10 comments 0 points Most recent by ChrisL August 2017Ask the Cromwell + WDL Team
• Best practices for large scatter operations

  Answered 163 views 4 comments 0 points Most recent by ChrisL August 2017Ask the Cromwell + WDL Team
• Reduce verbosity of cromwell run

  Accepted Answer 98 views 2 comments 0 points Most recent by Ruchi August 2017Ask the Cromwell + WDL Team
• runnig wdl workflow with cromwell on google cloud

  Answered 268 views 5 comments 0 points Most recent by idan_g August 2017Ask the Cromwell + WDL Team
• running wdl on google genomics

  Accepted Answer 257 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 70 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 121 views 1 comment 0 points Most recent by kshakir July 2017Ask the Cromwell + WDL Team
• cromwell on sge with containers

  Answered 103 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 234 views 12 comments 0 points Most recent by jweinstk July 2017Ask the Cromwell + WDL Team
• stopping a pipeline using cromwell API

  Accepted Answer 202 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 279 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 77 views 2 comments 0 points Most recent by Migwell June 2017Ask the Cromwell + WDL Team