Ask the Cromwell + WDL Team

Discussion List

• New CloudSQL database fails initial migration

  Accepted Answer 52 views 1 comment 0 points Most recent by danb October 2018Ask the Cromwell + WDL Team
• Docker support for LSF backend

  Answered 90 views 1 comment 0 points Most recent by Ruchi December 2018Ask the Cromwell + WDL Team
• Recursive folders creation when running "Data Pre-Processing" workflow

  Answered 114 views 1 comment 0 points Most recent by hkeward November 2018Ask the Cromwell + WDL Team
• unable to do docker lookup

  Accepted Answer 80 views 0 comments 0 points Started by afrieden October 2018 Ask the Cromwell + WDL Team
• Import workflow - failed after changing from cromwell v32 to v36

  Answered 151 views 1 comment 0 points Most recent by dplichta October 2018Ask the Cromwell + WDL Team
• How to realize and control scatter-gather function with Cromwell in a VM machine

  Answered 71 views 1 comment 0 points Most recent by Angry_Panda October 2018Ask the Cromwell + WDL Team
• How are files and auto-scaling supposed to work on AWS?

  Accepted Answer 57 views 0 comments 0 points Started by seandavi October 2018 Ask the Cromwell + WDL Team
• submit via SSH

  Answered 46 views 1 comment 0 points Most recent by staaan October 2018Ask the Cromwell + WDL Team
• How can I use scatter/gather on a set of mixed paired-end and single-end libraries?

  Accepted Answer 38 views 0 comments 0 points Started by seandavi October 2018 Ask the Cromwell + WDL Team
• Cromwell + Google Cloud MySQL

  Accepted Answer 84 views 1 comment 0 points Most recent by mooses October 2018Ask the Cromwell + WDL Team
• https://ketodiettrial.com/dermavix-spain/

  Accepted Answer 35 views 0 comments 0 points Started by swhanealsh October 2018 Ask the Cromwell + WDL Team
• How to choose backend in WDL file

  Accepted Answer 96 views 1 comment 0 points Most recent by staaan October 2018Ask the Cromwell + WDL Team
• read_csv() could not read file

  Accepted Answer 44 views 0 comments 0 points Started by shenwl October 2018 Ask the Cromwell + WDL Team
• Run/Stop tasks in a WDL script

  Question 31 views 1 comment 0 points Most recent by seandavi October 2018Ask the Cromwell + WDL Team
• Editing a configuration file doesn't work

  Answered 129 views 3 comments 0 points Most recent by OggieM October 2018Ask the Cromwell + WDL Team
• Can't use named inputs

  Accepted Answer 35 views 0 comments 0 points Started by CarlosBorroto October 2018 Ask the Cromwell + WDL Team
• Running Cromwell on AWS Batch, using both S3 and GC filesystems

  Accepted Answer 202 views 0 comments 0 points Started by Migwell October 2018 Ask the Cromwell + WDL Team
• Does cromwell prioritise finishing workflows

  Accepted Answer 45 views 5 comments 0 points Most recent by dario_romagnoli January 17Ask the Cromwell + WDL Team
• SamToFastqAndBwaMem error when running processing-for-variant-discovery-gatk4.wdl locally

  Answered 376 views 18 comments 0 points Most recent by jaideepjoshi February 7Ask the Cromwell + WDL Team
• Where to find cromwell-genomics-ami.cloud-init.yaml or an example of it?

  Accepted Answer 70 views 2 comments 0 points Most recent by Ruchi November 2018Ask the Cromwell + WDL Team
• Relative path in json files for cromwell

  Accepted Answer 150 views 0 comments 1 point Started by DivyKangeyan October 2018 Ask the Cromwell + WDL Team
• cromwell on AWS: using instance storage

  Accepted Answer 51 views 0 comments 0 points Started by ilya October 2018 Ask the Cromwell + WDL Team
• cromwell is skipping a scatter call

  Answered 44 views 3 comments 0 points Most recent by alphahmed October 2018Ask the Cromwell + WDL Team
• Can I put variable in configuration file (for backend)

  Accepted Answer 91 views 3 comments 0 points Most recent by staaan October 2018Ask the Cromwell + WDL Team