cromwell

• String expanding to array after scatter block

  Answered 12 views 1 comment 0 points Most recent by ChrisL September 21Ask the WDL team
• Localization via hard link has failed

  Answered 32 views 9 comments 0 points Most recent by Redmar_van_den_Berg September 19Ask the WDL team
• color in the output to screen from cromwell run

  Answered 81 views 20 comments 0 points Most recent by blueskypy September 14Ask the WDL team
• Using Docker Content Trust with Cromwell

  Answered 34 views 6 comments 0 points Most recent by mcovarr September 8Ask the WDL team
• Is it possible that WDLTool accepts filenames that start with numbers and contain underscores?

  Answered 22 views 2 comments 0 points Most recent by Yatros September 5Ask the WDL team
• Easy fix in the documentation in hte Running section

  Answered 14 views 1 comment 0 points Most recent by Geraldine_VdAuwera August 31Ask the WDL team
• Retrieving metadata for large workflows

  Answered 36 views 6 comments 0 points Most recent by mcovarr August 28Ask the WDL team
• Cromwell workflows appear hung

  Answered 66 views 11 comments 0 points Most recent by mcovarr August 28Ask the WDL team
• Feature Request: Add username to database

  Answered 45 views 13 comments 0 points Most recent by Ruchi August 17Ask the WDL team
• 热烈欢迎我们的中国朋友 / A warm welcome to our Chinese friends

  245 views 7 comments 2 points Most recent by xiaoshidi August 17Announcements
• How to know which job failed in continuewhenpossible mode?

  Answered 16 views 3 comments 0 points Most recent by ChrisL August 11Ask the WDL team
• WDL fail with NoSuchFileException, but the file exists

  Answered 79 views 12 comments 0 points Most recent by awacs August 10Ask the WDL team
• Scatter Gather and Spark together

  Answered 61 views 2 comments 1 point Most recent by Geraldine_VdAuwera August 9Ask the WDL team
• Syntax change in Cromwell v29 command line

  13 views 0 comments 0 points Started by Geraldine_VdAuwera August 6 WDL Announcements
• [cromwell 28_2] MySQL database issue: Specified key was too long; max key length is 1000 bytes

  Answered 32 views 10 comments 0 points Most recent by ChrisL August 4Ask the WDL team
• Best practices for large scatter operations

  Answered 44 views 4 comments 0 points Most recent by ChrisL August 3Ask the WDL team
• Reduce verbosity of cromwell run

  Answered 31 views 2 comments 0 points Most recent by Ruchi August 3Ask the WDL team
• runnig wdl workflow with cromwell on google cloud

  Answered 68 views 5 comments 0 points Most recent by idan_g August 2Ask the WDL team
• connection reset by peer, defining memory is not working

  Answered 33 views 1 comment 0 points Most recent by Geraldine_VdAuwera July 31Ask the WDL team
• running wdl on google genomics

  Answered 64 views 6 comments 0 points Most recent by afrieden July 27Ask the WDL team
• read_tsv failed because the file was too big

  Answered 19 views 1 comment 0 points Most recent by danb July 27Ask the WDL team
• Forcing cromwell to submit all possible jobs at once

  Answered 26 views 1 comment 0 points Most recent by kshakir July 26Ask the WDL team
• cromwell on sge with containers

  Answered 30 views 1 comment 0 points Most recent by jgentry July 21Ask the WDL team
• cromwell error: failed to find index Success on array

  Answered 104 views 12 comments 0 points Most recent by jweinstk July 18Ask the WDL team
• stopping a pipeline using cromwell API

  Answered 75 views 11 comments 0 points Most recent by ChrisL July 13Ask the WDL team
• Deleting intermediate files

  Answered 78 views 10 comments 0 points Most recent by Ruchi July 11Ask the WDL team
• Cromwell support for docker with -w option to change current working directory inside container

  Answered 56 views 3 comments 0 points Most recent by ChrisL July 11Ask the WDL team
• getting tail of the array

  Answered 31 views 2 comments 0 points Most recent by ChrisL July 5Ask the WDL team
• Logging variable values at each stage of the workflow

  Answered 28 views 2 comments 0 points Most recent by Migwell June 30Ask the WDL team
• MySQL cache migration when updating Cromwell version

  Answered 23 views 5 comments 0 points Most recent by danb June 29Ask the WDL team
• Question on caching

  Answered 28 views 5 comments 0 points Most recent by danb June 28Ask the WDL team
• [warn] Localization via hard link has failed Invalid cross-device link

  Answered 164 views 14 comments 0 points Most recent by mcovarr June 22Ask the WDL team
• Setting Up a Cromwell VM

  Answered 61 views 5 comments 0 points Most recent by Geraldine_VdAuwera June 20Ask the WDL team
• Diagnosing call caching behavior

  Answered 69 views 5 comments 0 points Most recent by mcovarr June 20Ask the WDL team
• Documentation on cromwell database mapping

  Answered 29 views 1 comment 0 points Most recent by Ruchi June 19Ask the WDL team
• Selectively disable call caching?

  Answered 52 views 1 comment 0 points Most recent by Ruchi June 14Ask the WDL team
• How to Query for Custom Labels in Cromwell

  Answered 81 views 6 comments 0 points Most recent by Ruchi June 13Ask the WDL team
• Docker image hashing issues in some scenarios with TES backend

  Answered 49 views 1 comment 0 points Most recent by Ruchi May 30Ask the WDL team
• Cromwell won't run, waiting for changelog lock

  Answered 53 views 1 comment 0 points Most recent by ChrisL May 26Ask the WDL team
• Is this error caused by a job submission failure?

  Answered 73 views 2 comments 0 points Most recent by jgentry May 17Ask the WDL team
• Cromwell I/O: Highway to the Cloud

  59 views 0 comments 0 points Started by Thib May 16 WDL Announcements
• Method permissions do not propagate across snapshots

  Answered 24 views 2 comments 0 points Most recent by Geraldine_VdAuwera April 26Ask the FireCloud Team
• Is there a tool for job metadata visualization?

  Answered 79 views 3 comments 0 points Most recent by mmah April 26Ask the WDL team
• Can I retry job submissions that sometimes fail?

  Answered 82 views 3 comments 0 points Most recent by Geraldine_VdAuwera April 22Ask the WDL team
• [WDL][Cromwell[ Mounting a directory to the docker for access.

  Answered 138 views 7 comments 0 points Most recent by deconti April 21Ask the GATK team
• Why is only one call allowed for a task even when different arguments are used?

  Answered 41 views 1 comment 0 points Most recent by Geraldine_VdAuwera April 19Ask the WDL team
• Race condition for simple script causing a job to run forever?

  Answered 169 views 11 comments 0 points Most recent by mcovarr April 12Ask the WDL team
• Cromwell 26: Retrying for you

  126 views 0 comments 2 points Started by KateVoss April 7 WDL Announcements
• Supported features of FC/Cromwell/WDL

  Answered 48 views 1 comment 0 points Most recent by Geraldine_VdAuwera April 6Ask the FireCloud Team
• What is stored in the SQL database for call caching?

  Answered 58 views 1 comment 0 points Most recent by ChrisL April 5Ask the WDL team
• How much memory does Cromwell need for input or output files?

  Question 110 views 3 comments 0 points Most recent by mmah April 3Ask the WDL team
• WDL pipeline can't parse write_lines(Array[File]) on Google Cloud

  Answered 64 views 3 comments 0 points Most recent by Geraldine_VdAuwera March 31Ask the WDL team
• How can a method configuration locate a file generated by WDL method ${write_lines(Array[File])}?

  Question 395 views 18 comments 0 points Most recent by gordon123 March 23Ask the FireCloud Team
• TESting, TESting, 1 2 3...

  94 views 0 comments 0 points Started by jgentry March 20 WDL Announcements
• cromwell server and mysql database configuration questions

  Answered 118 views 1 comment 0 points Most recent by jgentry March 17Ask the WDL team
• [WDL][Cromwell] Submitting a workflow with a subworkflow to the cloud.

  Answered 155 views 2 comments 1 point Most recent by deconti March 8Ask the GATK team
• Cromwell 25 release

  157 views 1 comment 0 points Most recent by KateVoss February 23WDL Announcements
• Announcing the WDL Blog!

  65 views 1 comment 1 point Most recent by KateVoss February 22WDL Announcements
• WDL: how to input and scatter an Array[Object] file ("Can't index" error)

  Answered 249 views 1 comment 0 points Most recent by mcovarr January 12Ask the WDL team
• Cromwell status failed during WDL script running bwa mem

  Answered 243 views 5 comments 0 points Most recent by EADG January 11Ask the WDL team
• Usage of WDL objects and the read_objects function

  Answered 179 views 4 comments 0 points Most recent by mcovarr January 3Ask the WDL team
• Can I specify additional parameters for the Cromwell submit configuration based on each task?

  Answered 115 views 1 comment 0 points Most recent by Thib December 2016Ask the WDL team
• LSF support in Cromwell

  Answered 200 views 3 comments 0 points Most recent by ink December 2016Ask the WDL team
• can't launch workflow

  Answered 124 views 10 comments 0 points Most recent by frcldtest December 2016Ask the FireCloud Team
• Task to Simply Collect Output Files

  Answered 140 views 4 comments 1 point Most recent by KateN December 2016Ask the WDL team
• Can a biochemist with one Python course under her belt start running analyses in the cloud?

  243 views 0 comments 0 points Started by shlee November 2016 Announcements
• Cromwell config issue

  Answered 222 views 4 comments 0 points Most recent by Geminghui November 2016Ask the WDL team
• Cromwell on Cluster

  Answered 224 views 4 comments 0 points Most recent by shair_rosenberg October 2016Ask the WDL team
• Cromwell is very slow while running RealignerTargetCreator

  141 views 7 comments 0 points Most recent by Geraldine_VdAuwera October 2016Ask the WDL team
• BroadE FireCloud Tool Developers Workshop: August 12th, 2016

  212 views 0 comments 1 point Started by jneff August 2016 Presentations
• API batch endpoint HTTP response code problem

  Answered 103 views 2 comments 0 points Most recent by conradL July 2016Ask the WDL team
• Handling optional workflow input

  Answered 112 views 1 comment 0 points Most recent by KateN July 2016Ask the WDL team
• OutOfMemoryError when call caching is turned on

  Answered 77 views 1 comment 0 points Most recent by KateN July 2016Ask the WDL team
• docker usable by cromwell? what are the requirements? /bin/bash nor /bin/sh usable?

  Answered 187 views 5 comments 0 points Most recent by esalinas July 2016Ask the WDL team
• Where i can get task logs before task is completed?

  Answered 82 views 3 comments 0 points Most recent by KateN June 2016Ask the WDL team
• Running in server mode, jobs that have localization error become immortal

  Answered 118 views 2 comments 0 points Most recent by conradL June 2016Ask the WDL team
• FireCloud Workshop for Tool Developers: June 15th

  Announcement 104 views 0 comments 0 points Started by jneff May 2016 FireCloud
• batch endpoint

  Answered 126 views 5 comments 0 points Most recent by Geraldine_VdAuwera May 2016Ask the WDL team
• declarations that refer to task outputs

  Answered 99 views 2 comments 0 points Most recent by stekaz April 2016Ask the WDL team
• The Art of the Pipeline: Introducing Cromwell + WDL

  2.6K views 1 comment 1 point Most recent by Geraldine_VdAuwera April 2016Announcements
• Tool Developers

  266 views 0 comments 0 points Started by jneff March 2016 Frequently Asked Questions
• Which workflow execution engines support WDL? What is Cromwell?

  213 views 0 comments 0 points Started by Geraldine_VdAuwera February 2016 Frequently Asked Questions
• cromwell local execution takes up too much disk space

  Answered 156 views 1 comment 0 points Most recent by birger February 2016Ask the FireCloud Team
• Tool Developer Basics

  177 views 0 comments 0 points Started by Geraldine_VdAuwera January 2016 Help Topics
• (howto) Run a WDL script via Cromwell on a local machine (e.g. your laptop)

  163 views 0 comments 0 points Started by Geraldine_VdAuwera December 2015 Tutorials