Task #13215

Story #13216: Write phasing imputation workflow

Write phasing workflow with eagle v2.4

Added by Jiayong Li over 1 year ago. Updated over 1 year ago.

Status:
Resolved
Priority:
Normal
Assigned To:
Start date:
03/22/2018
Due date:
% Done:

100%

Estimated time:
0.00 h

Description

Phasing.tar.gz (1.53 KB) Phasing.tar.gz Jiayong Li, 03/21/2018 03:37 PM

Subtasks

Task #13263: ReviewResolvedAbram Connelly


Related issues

Related to Arvados - Bug #13252: [CWL] RunInSingleContainer requirement errors on DockerRequirement even when no such requirement is specifiedNew

History

#1 Updated by Jiayong Li over 1 year ago

  • Status changed from New to In Progress

#2 Updated by Jiayong Li over 1 year ago

  • Description updated (diff)
  • Due date set to 03/16/2018
  • Assigned To set to Jiayong Li

#3 Updated by Jiayong Li over 1 year ago

  • Parent task set to #13216

#4 Updated by Jiayong Li over 1 year ago

  • Start date set to 03/16/2018

#5 Updated by Jiayong Li over 1 year ago

Note that I had to make sure the input vcf has ref/alt to be upper case in order for eagle 2.4 to work. See input collection https://workbench.su92l.arvadosapi.com/collections/su92l-4zz18-7mgp8zxt2tap39a

#6 Updated by Jiayong Li over 1 year ago

I'm trying to run a workflow in a single container but it failed. https://workbench.su92l.arvadosapi.com/container_requests/su92l-xvhdp-8d7o1hq6mnnri85

I've got the following error.

2018-03-21T00:06:23.256283830Z [step eagle] start
2018-03-21T00:06:23.260142930Z Exception on step 'eagle'
2018-03-21T00:06:23.260701530Z Cannot make scatter job: --no-container, but this CommandLineTool has DockerRequirement under 'requirements'.
2018-03-21T00:06:23.261063530Z Workflow cannot make any more progress.
2018-03-21T00:06:23.261720930Z Final process status is permanentFail

However, the script eagle.cwl does NOT have DockerRequirement.

See the attached tar ball for the cwl scripts. The command I was using:

arvados-cwl-runner --api=containers --submit --no-wait --project-uuid su92l-j7d0g-huzwo8ptw745hjx phasing-wf.cwl yml/phasing-GS12877.yml

Note that without the RunInSingleContainer requirement, the workflow completed. https://workbench.su92l.arvadosapi.com/container_requests/su92l-xvhdp-94180nzfj7yz6q5

For the record

arvados-cwl-runner --version
/usr/bin/arvados-cwl-runner 1.0.20180223182850, arvados-python-client 0.1.20180223161544, cwltool 1.0.20180130110340

#7 Updated by Jiayong Li over 1 year ago

  • Related to Bug #13252: [CWL] RunInSingleContainer requirement errors on DockerRequirement even when no such requirement is specified added

#8 Updated by Jiayong Li over 1 year ago

As Peter have noted, the run succeeded after moving the docker requirement under hints. https://workbench.su92l.arvadosapi.com/container_requests/su92l-xvhdp-tbz5tqgxp1p5x4h

In other words, changing

cwlVersion: v1.0
class: Workflow
$namespaces:
  arv: "http://arvados.org/cwl#" 
requirements:
  arv:RunInSingleContainer: {}
  DockerRequirement:
    dockerPull: l7g-ml/phasing

to
cwlVersion: v1.0
class: Workflow
$namespaces:
  arv: "http://arvados.org/cwl#" 
requirements:
  arv:RunInSingleContainer: {}
hints:
  DockerRequirement:
    dockerPull: l7g-ml/phasing

The above workflow phases the input vcf across the reference panel, which is split up by chromosomes, and then concatenate them. The non-RunInSingleContainer is here https://workbench.su92l.arvadosapi.com/container_requests/su92l-xvhdp-rxjg9h5sm9xybiv

#9 Updated by Jiayong Li over 1 year ago

  • Status changed from In Progress to Feedback

branch 13216-phasing-imputation-workflow, commit fd338cefafe44fc2386f3be04b65363cba0f487d

#10 Updated by Abram Connelly over 1 year ago

Review of fd338cefafe44fc2386f3be04b65363cba0f487d.

There's a spurious space under 'inputs: ... chr:' in phaseing-wf.cwl but otherwise looks good to merge.

#11 Updated by Jiayong Li over 1 year ago

Fixed and merged.

#12 Updated by Jiayong Li over 1 year ago

  • Status changed from Feedback to Resolved

#13 Updated by Jiayong Li over 1 year ago

  • Subject changed from Write phasing workflow with beagle v2.4 to Write phasing workflow with eagle v2.4
  • Description updated (diff)

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