cromwell

Discussion List

• long wait time between workflow finishing and getting final workflow status

  Question 60 views 2 comments 0 points Most recent by ChrisL June 13Ask the WDL team
• Why does this work?

  Answered 22 views 4 comments 0 points Most recent by ChrisL June 12Ask the WDL team
• Tabix-incompatible file creation times

  Answered 13 views 2 comments 0 points Most recent by KateN June 11Ask the FireCloud Team
• Can Cromwell limit the number of concurrent jobs for a particular task?

  Answered 19 views 1 comment 0 points Most recent by Thib June 2Ask the WDL team
• not-working mutect2 WDL pipeline.

  Answered 20 views 1 comment 0 points Most recent by Sheila June 1Ask the GATK team
• Can I query by multiple labels using json POST?

  Question 11 views 0 comments 0 points Started by lkajan May 31 Ask the WDL team
• You can't spell Cromwell without CWL

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

  Answered 12 views 1 comment 0 points Most recent by Thib May 23Ask the WDL team
• Call QueuedInCromwell, Job Running?

  Accepted Answer 208 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 32 views 0 comments 0 points Started by santiagorevale May 18 Ask the WDL team
• Is this error caused by a job submission failure?

  Accepted Answer 121 views 7 comments 1 point Most recent by alongalor May 17Ask the WDL team
• Pre-start hook?

  Answered 24 views 2 comments 0 points Most recent by edpark_clearlabs May 16Ask the WDL team
• Building cromwell 31

  Accepted Answer 21 views 9 comments 0 points Most recent by danb May 7Ask the WDL team
• Is the a dev guide to writing cromwell backends?

  Accepted Answer 20 views 2 comments 0 points Most recent by mathias1 May 7Ask the WDL team
• How do I cite tools such as firecloud, WDL and cromwell?

  Accepted Answer 55 views 2 comments 0 points Most recent by DivyKangeyan May 7Ask the FireCloud Team
• Running Cromwell

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

  Accepted Answer 114 views 2 comments 0 points Most recent by bshifaw April 17Ask the GATK team
• Bug: Queued in Cromwell

  Accepted Answer 87 views 4 comments 0 points Most recent by mcovarr April 12Ask the FireCloud Team
• [WDL][Cromwell[ Mounting a directory to the docker for access.

  Accepted Answer 321 views 10 comments 0 points Most recent by ChrisL April 3Ask the GATK team
• extraneous copies of input files

  Answered 44 views 4 comments 0 points Most recent by Thib March 30Ask the WDL team
• Deleting intermediate files

  Answered 240 views 12 comments 0 points Most recent by dinvlad March 9Ask the WDL team
• getting tail of the array

  Answered 77 views 4 comments 0 points Most recent by ChrisL March 3Ask the WDL team
• Multiple workflow languages coming to Cromwell, starting with CWL

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

  Accepted Answer 80 views 3 comments 0 points Most recent by DivyKangeyan February 26Ask the WDL team
• Any way to set concurrent-job-limit dynamically?

  Accepted Answer 27 views 4 comments 0 points Most recent by Thib February 22Ask the WDL team
• How much memory does Cromwell need for input or output files?

  Accepted Answer 184 views 4 comments 0 points Most recent by kshakir February 8Ask the WDL team
• Cromwell call-caching Failed to hash error

  Answered 24 views 1 comment 0 points Most recent by kshakir February 8Ask the WDL team
• Problem with running gatk haplotypecaller in cromwell with spark backend

  Answered 257 views 1 comment 0 points Most recent by henderj8 February 8Ask the WDL team
• How to import workflows that also have imports themselves?

  Answered 77 views 5 comments 0 points Most recent by rhpvorderman February 8Ask the WDL team
• Cromwell call-caching Failed to hash error

  Answered 57 views 4 comments 0 points Most recent by jsoto January 18Ask the WDL team
• GATK on FireCloud

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

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

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

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

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

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

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

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

  104 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 52 views 3 comments 1 point Most recent by ChrisL December 2017Ask the WDL team
• Any way (or plan) ro launch WDL in FireCloud without creating workspace?

  Answered 72 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 93 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 25 views 1 comment 0 points Most recent by dpark November 2017Ask the WDL team
• String? type in output section

  Answered 40 views 3 comments 0 points Most recent by ChrisL October 2017Ask the WDL team
• connection reset by peer, defining memory is not working

  Answered 113 views 5 comments 0 points Most recent by shlee October 2017Ask the WDL team
• 热烈欢迎我们的中国朋友 / A warm welcome to our Chinese friends

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

  Answered 116 views 11 comments 0 points Most recent by kshakir September 2017Ask the WDL team
• Bug: Cromwell removes empty spaces from WDL when creating exec.sh

  Accepted Answer 52 views 3 comments 0 points Most recent by Tiffany_at_Broad September 2017Ask the WDL team
• String expanding to array after scatter block

  Accepted Answer 25 views 1 comment 0 points Most recent by ChrisL September 2017Ask the WDL team
• color in the output to screen from cromwell run

  Accepted Answer 122 views 20 comments 0 points Most recent by blueskypy September 2017Ask the WDL team
• Using Docker Content Trust with Cromwell

  Answered 83 views 6 comments 0 points Most recent by mcovarr September 2017Ask the WDL team
• Is it possible that WDLTool accepts filenames that start with numbers and contain underscores?

  Accepted Answer 43 views 2 comments 0 points Most recent by Yatros September 2017Ask the WDL team
• Easy fix in the documentation in hte Running section

  Accepted Answer 32 views 1 comment 0 points Most recent by Geraldine_VdAuwera August 2017Ask the WDL team
• Retrieving metadata for large workflows

  Accepted Answer 65 views 6 comments 0 points Most recent by mcovarr August 2017Ask the WDL team
• Cromwell workflows appear hung

  Accepted Answer 118 views 11 comments 0 points Most recent by mcovarr August 2017Ask the WDL team
• Feature Request: Add username to database

  Accepted Answer 60 views 13 comments 0 points Most recent by Ruchi August 2017Ask the WDL team
• How to know which job failed in continuewhenpossible mode?

  Answered 52 views 3 comments 0 points Most recent by ChrisL August 2017Ask the WDL team
• WDL fail with NoSuchFileException, but the file exists

  Accepted Answer 212 views 12 comments 0 points Most recent by awacs August 2017Ask the WDL team
• Scatter Gather and Spark together

  Accepted Answer 221 views 2 comments 1 point Most recent by Geraldine_VdAuwera August 2017Ask the WDL team
• Syntax change in Cromwell v29 command line

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

  Accepted Answer 120 views 10 comments 0 points Most recent by ChrisL August 2017Ask the WDL team
• Best practices for large scatter operations

  Answered 118 views 4 comments 0 points Most recent by ChrisL August 2017Ask the WDL team
• Reduce verbosity of cromwell run

  Accepted Answer 71 views 2 comments 0 points Most recent by Ruchi August 2017Ask the WDL team
• runnig wdl workflow with cromwell on google cloud

  Answered 173 views 5 comments 0 points Most recent by idan_g August 2017Ask the WDL team
• running wdl on google genomics

  Accepted Answer 159 views 6 comments 0 points Most recent by afrieden July 2017Ask the WDL team
• read_tsv failed because the file was too big

  Answered 38 views 1 comment 0 points Most recent by danb July 2017Ask the WDL team
• Forcing cromwell to submit all possible jobs at once

  Answered 84 views 1 comment 0 points Most recent by kshakir July 2017Ask the WDL team
• cromwell on sge with containers

  Answered 77 views 1 comment 0 points Most recent by jgentry July 2017Ask the WDL team
• cromwell error: failed to find index Success on array

  Accepted Answer 173 views 12 comments 0 points Most recent by jweinstk July 2017Ask the WDL team
• stopping a pipeline using cromwell API

  Accepted Answer 143 views 11 comments 0 points Most recent by ChrisL July 2017Ask the WDL team
• Cromwell support for docker with -w option to change current working directory inside container

  Answered 156 views 3 comments 0 points Most recent by ChrisL July 2017Ask the WDL team
• Logging variable values at each stage of the workflow

  Accepted Answer 50 views 2 comments 0 points Most recent by Migwell June 2017Ask the WDL team
• MySQL cache migration when updating Cromwell version

  Answered 36 views 5 comments 0 points Most recent by danb June 2017Ask the WDL team
• Question on caching

  Accepted Answer 52 views 5 comments 0 points Most recent by danb June 2017Ask the WDL team
• [warn] Localization via hard link has failed Invalid cross-device link

  Answered 309 views 14 comments 0 points Most recent by mcovarr June 2017Ask the WDL team
• Setting Up a Cromwell VM

  Answered 88 views 5 comments 0 points Most recent by Geraldine_VdAuwera June 2017Ask the WDL team
• Diagnosing call caching behavior

  Accepted Answer 112 views 5 comments 0 points Most recent by mcovarr June 2017Ask the WDL team
• Documentation on cromwell database mapping

  Accepted Answer 50 views 1 comment 0 points Most recent by Ruchi June 2017Ask the WDL team
• Selectively disable call caching?

  Accepted Answer 80 views 1 comment 0 points Most recent by Ruchi June 2017Ask the WDL team
• How to Query for Custom Labels in Cromwell

  Accepted Answer 108 views 6 comments 0 points Most recent by Ruchi June 2017Ask the WDL team
• Docker image hashing issues in some scenarios with TES backend

  Answered 65 views 1 comment 0 points Most recent by Ruchi May 2017Ask the WDL team
• Cromwell won't run, waiting for changelog lock

  Accepted Answer 121 views 1 comment 0 points Most recent by ChrisL May 2017Ask the WDL team
• Cromwell I/O: Highway to the Cloud

  99 views 0 comments 0 points Started by Thib May 2017 WDL Announcements
• Method permissions do not propagate across snapshots

  Answered 36 views 2 comments 0 points Most recent by Geraldine_VdAuwera April 2017Ask the FireCloud Team
• Is there a tool for job metadata visualization?

  Accepted Answer 117 views 3 comments 0 points Most recent by mmah April 2017Ask the WDL team
• Can I retry job submissions that sometimes fail?

  Accepted Answer 132 views 3 comments 0 points Most recent by Geraldine_VdAuwera April 2017Ask the WDL team
• Why is only one call allowed for a task even when different arguments are used?

  Accepted Answer 71 views 1 comment 0 points Most recent by Geraldine_VdAuwera April 2017Ask the WDL team
• Race condition for simple script causing a job to run forever?

  Accepted Answer 303 views 11 comments 0 points Most recent by mcovarr April 2017Ask the WDL team
• Cromwell 26: Retrying for you

  169 views 0 comments 2 points Started by KateVoss April 2017 WDL Announcements
• Supported features of FC/Cromwell/WDL

  Accepted Answer 65 views 1 comment 0 points Most recent by Geraldine_VdAuwera April 2017Ask the FireCloud Team
• What is stored in the SQL database for call caching?

  Accepted Answer 82 views 1 comment 0 points Most recent by ChrisL April 2017Ask the WDL team
• WDL pipeline can't parse write_lines(Array[File]) on Google Cloud

  Accepted Answer 95 views 3 comments 0 points Most recent by Geraldine_VdAuwera March 2017Ask the WDL team
• How can a method configuration locate a file generated by WDL method ${write_lines(Array[File])}?

  Question 571 views 18 comments 0 points Most recent by gordon123 March 2017Ask the FireCloud Team
• TESting, TESting, 1 2 3...

  167 views 0 comments 0 points Started by jgentry March 2017 WDL Announcements
• cromwell server and mysql database configuration questions

  Answered 209 views 1 comment 0 points Most recent by jgentry March 2017Ask the WDL team
• [WDL][Cromwell] Submitting a workflow with a subworkflow to the cloud.

  Accepted Answer 267 views 2 comments 1 point Most recent by deconti March 2017Ask the GATK team
• Cromwell 25 release

  171 views 1 comment 0 points Most recent by KateVoss February 2017WDL Announcements
• Announcing the WDL Blog!

  80 views 1 comment 1 point Most recent by KateVoss February 2017WDL Announcements
• WDL: how to input and scatter an Array[Object] file ("Can't index" error)

  Accepted Answer 454 views 1 comment 0 points Most recent by mcovarr January 2017Ask the WDL team
• Cromwell status failed during WDL script running bwa mem

  Accepted Answer 339 views 5 comments 0 points Most recent by EADG January 2017Ask the WDL team