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

Back to business #679

Merged
merged 4 commits into from
Jul 22, 2022
Merged

Back to business #679

merged 4 commits into from
Jul 22, 2022

Conversation

maxulysse
Copy link
Member

PR checklist

  • 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 pipeline conventions in the contribution docs
    • If necessary, also make a PR on the nf-core/sarek branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@github-actions
Copy link

github-actions bot commented Jul 22, 2022 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3332764

+| ✅ 145 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.

❔ Tests ignored:

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

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-07-22 08:35:40

@asp8200
Copy link
Contributor

asp8200 commented Jul 22, 2022

@maxulysse : Is the file docs/images/sarek_indices_subway.png getting updated with this PR? It seems that the new png-file still refers to Sarek v3.0 - is that as it should be? (I couldn't figure out how to place this comment directly at the file, so I just put it here 😁 )

image

@maxulysse
Copy link
Member Author

True, but at the moment, not sure if the next release will be 3.0.1 or 3.1, so I prefered to stay with 3.0 for now

asp8200
asp8200 approved these changes Jul 22, 2022
View reviewed changes
Copy link
Contributor

@asp8200 asp8200 left a comment

Choose a reason for hiding this comment

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

LGTM

jfy133
jfy133 approved these changes Jul 22, 2022
View reviewed changes
Copy link
Member

@jfy133 jfy133 left a comment

Choose a reason for hiding this comment

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

for the submway

I would still recommend rrotating the nf-core/sarek logo and image title to normal Left to right, you can move the legend to right justified.

But otherwise everything looks OK

You have lots of white space you cna use, and the current 90 rotation is dfficult to read

@maxulysse
Copy link
Member Author

You have lots of white space you cna use, and the current 90 rotation is dfficult to read

I do like that actually

@maxulysse maxulysse merged commit 5d53e49 into nf-core:dev Jul 22, 2022
@maxulysse maxulysse deleted the dev_3plusdev branch July 22, 2022 09:16
FriederikeHanssen
FriederikeHanssen reviewed Jul 22, 2022
View reviewed changes
README.md
@@ -23,7 +23,7 @@

The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!

<!-- On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/sarek/results). -->
On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/sarek/results).
Copy link
Contributor

Choose a reason for hiding this comment

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

🤦‍♀️ well there is always something to forget

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

@FriederikeHanssen FriederikeHanssen FriederikeHanssen left review comments

@asp8200 asp8200 asp8200 approved these changes

@jfy133 jfy133 jfy133 approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
4 participants
@maxulysse @asp8200 @FriederikeHanssen @jfy133