Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Updating the deepvariant module #427

Merged
merged 1 commit into from
Sep 16, 2021
Merged

Updating the deepvariant module #427

merged 1 commit into from
Sep 16, 2021

Conversation

abhi18av
Copy link
Member

This PR updates the deepvariant module with the changes incorporated in nf-core/modules#572

@abhi18av abhi18av self-assigned this Sep 15, 2021
@github-actions
Copy link

github-actions bot commented Sep 15, 2021 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit cefd07d

+| ✅ 135 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗  10 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version mentioned in Quick Start section.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in main.nf: Named file extensions MUST be emitted for ALL output channels
  • pipeline_todos - TODO string in main.nf: List additional required output channels/values here
  • pipeline_todos - TODO string in main.nf: It MUST be possible to pass additional parameters to the tool as a command-line string via the "$ioptions.args" variable
  • pipeline_todos - TODO string in main.nf: If the tool supports multi-threading then you MUST provide the appropriate parameter

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.1
  • Run at 2021-09-15 18:32:26

@maxulysse
Copy link
Member

Looks good, but if you're updating the module, let's wait for the PR to be merged, and then let's install the module with the nf-core command

@abhi18av
Copy link
Member Author

... but if you're updating the module, let's wait for the PR to be merged,

Actually, I'm not sure when it'd be merged since the conda package for deepvariant is problematic and without it the tests wouldn't pass.

This is the reason I have raised this PR so as to keep this code in shape till we have a merge.

@maxulysse
Copy link
Member

I see.
I made some comments on the modules PR, and I pinged the modules team about the conda issues

maxulysse
maxulysse approved these changes Sep 16, 2021
View reviewed changes
Copy link
Member

@maxulysse maxulysse left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

LGTM

@maxulysse maxulysse merged commit 57c4140 into dev Sep 16, 2021
@maxulysse maxulysse deleted the abhinav/update-deepvariant branch September 16, 2021 10:05
@abhi18av
Copy link
Member Author

Thanks @maxulysse 😊

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@maxulysse maxulysse maxulysse approved these changes

Assignees

@abhi18av abhi18av

Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@abhi18av @maxulysse