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.

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

Unicycler with long read input #1041

Merged
merged 5 commits into from
Nov 15, 2021
Merged

Unicycler with long read input #1041

merged 5 commits into from
Nov 15, 2021

Conversation

d4straub
Copy link
Contributor

@d4straub d4straub commented Nov 8, 2021

PR checklist

Closes #890

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd
    • PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd
    • PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd

@d4straub d4straub added WIP Work in progress update module labels Nov 8, 2021
@mahesh-panchal
Copy link
Member

mahesh-panchal commented Nov 9, 2021

We're having this problem too. It's on the Bioconda end. My colleagues say the channel index is corrupted and someone is trying to fix it.

https://gitter.im/bioconda/Lobby?at=618a182d38377967f4a0240d

@d4straub
Copy link
Contributor Author

d4straub commented Nov 9, 2021

Thanks! Will wait then 👍

@d4straub
Copy link
Contributor Author

d4straub commented Nov 10, 2021

Alright, so that is a new experience for me:

  • md5sums for singularity, docker and conda are all different
  • conda md5sums are stable
  • md5sums for singularity and docker are variable between runs

That means, singularity and docker will always fail right now when using md5sums. Should I remove md5sums? At least for conda md5sums are working though!

edit: will remove unstable md5sums (see below)

@d4straub d4straub added Ready for Review and removed WIP Work in progress labels Nov 10, 2021
modules/unicycler/main.nf Outdated Show resolved Hide resolved
Copy link
Member

@drpatelh drpatelh left a comment

Choose a reason for hiding this comment

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

💯

@drpatelh drpatelh merged commit 171a2a2 into nf-core:master Nov 15, 2021
@d4straub d4straub deleted the unicycler branch November 15, 2021 11:57
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
Development

Successfully merging this pull request may close these issues.

Unicycler should allow also long read and hybrid assembly
3 participants