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

Feature/nf secrets #343

Merged
merged 21 commits into from
Jan 22, 2024
Merged

Feature/nf secrets #343

merged 21 commits into from
Jan 22, 2024

Conversation

pbelmann
Copy link
Member

This PR enabled the use of Nextflows secrets feature. Instead of using one secrets mechanism in the aws.confg and a different one for s5cmd, it is now possible to set secrets uniformly.

Example:

nextflow secrets set S3_kegg_ACCESS XXXXXXXXXXXXXXX

PR review guidelines

Thank you for submitting this PR.

Before merge:

  • The PR must be reviewed by one of the team members.

  • Please check if anything in the Readme must be adjusted, or added (development-setup, production-setup, user-guide).

  • PRs with new modules or workflow interfaces must include tests according to the developer guidelines.

  • The new code is readable, well commented and should adhere to our developer guidelines.

  • Before merging it must be checked if a squash of commits is required.

@pbelmann pbelmann requested a review from bosterholz November 6, 2023 08:02
Copy link
Collaborator

@bosterholz bosterholz left a comment

Choose a reason for hiding this comment

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

Great, thanks!

example_params/fullPipelineSRAQC.yml Outdated Show resolved Hide resolved
@@ -1,5 +1,7 @@
tempdir: "tmp"
summary: false
s3SignIn: true
s3SignIn: true
Copy link
Collaborator

Choose a reason for hiding this comment

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

Double?

docs/pipeline_configuration.md Outdated Show resolved Hide resolved
@pbelmann pbelmann merged commit 99bac77 into dev Jan 22, 2024
1 of 15 checks passed
@pbelmann pbelmann deleted the feature/nf-secrets branch January 22, 2024 21:45
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants