Task #13215
closed
Idea #13216: Write phasing imputation workflow
Write phasing workflow with eagle v2.4
Added by Jiayong Li about 6 years ago. Updated about 6 years ago.
Description
- Build docker image with eagle v2.4 (https://data.broadinstitute.org/alkesgroup/Eagle/downloads/Eagle_v2.4.tar.gz)
- Write workflow scattering across reference panels
- Test workflow
Files
| Phasing.tar.gz (1.53 KB) Phasing.tar.gz | Jiayong Li, 03/21/2018 03:37 PM |
Related issues
Updated by Jiayong Li about 6 years ago
- Description updated (diff)
- Due date set to 03/16/2018
- Assigned To set to Jiayong Li
Updated by Jiayong Li about 6 years ago
- Start date set to 03/16/2018
eagle job on a single chromosome
https://workbench.su92l.arvadosapi.com/container_requests/su92l-xvhdp-fb92nf0vrknyfxs
Updated by Jiayong Li about 6 years 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
Updated by Jiayong Li about 6 years ago
- File Phasing.tar.gz Phasing.tar.gz added
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
Updated by Jiayong Li about 6 years ago
- Related to Bug #13252: [CWL] RunInSingleContainer requirement errors on DockerRequirement even when no such requirement is specified added
Updated by Jiayong Li about 6 years 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
Updated by Jiayong Li about 6 years ago
- Status changed from In Progress to Feedback
branch 13216-phasing-imputation-workflow, commit fd338cefafe44fc2386f3be04b65363cba0f487d
Updated by Abram Connelly about 6 years ago
Review of fd338cefafe44fc2386f3be04b65363cba0f487d.
There's a spurious space under 'inputs: ... chr:' in phaseing-wf.cwl but otherwise looks good to merge.
Updated by Jiayong Li about 6 years ago
- Status changed from Feedback to Resolved
Updated by Jiayong Li about 6 years ago
- Subject changed from Write phasing workflow with beagle v2.4 to Write phasing workflow with eagle v2.4
- Description updated (diff)