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

FEAT: Improve documentation for annotation cache #1248

Merged
merged 12 commits into from
Sep 28, 2023
Merged

FEAT: Improve documentation for annotation cache #1248

merged 12 commits into from
Sep 28, 2023

Conversation

maxulysse
Copy link
Member

WIP

@maxulysse maxulysse marked this pull request as draft September 19, 2023 12:26
@github-actions
Copy link

github-actions bot commented Sep 19, 2023 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9e3e91d

+| ✅ 147 tests passed       |+
#| ❔   8 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in WorkflowSarek.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-09-28 13:38:03

@maxulysse
Copy link
Member Author

website for annotation-cache: https://annotation-cache.github.io/

@maxulysse maxulysse marked this pull request as ready for review September 26, 2023 15:12
@maxulysse maxulysse mentioned this pull request Sep 27, 2023
Closed
FriederikeHanssen
FriederikeHanssen reviewed Sep 28, 2023
View reviewed changes
docs/usage.md Outdated Show resolved Hide resolved
@maxulysse @FriederikeHanssen
Update docs/usage.md
544e16c 
Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
maxulysse
maxulysse commented Sep 28, 2023
View reviewed changes
docs/usage.md Outdated Show resolved Hide resolved
FriederikeHanssen
FriederikeHanssen reviewed Sep 28, 2023
View reviewed changes
workflows/sarek.nf Outdated
if (params.snpeff_cache == "s3://annotation-cache/snpeff_cache") {
error("This path is not available within annotation-cache. Please check https://annotation-cache.github.io/ to create a request for it.")
} else {
error("Files within --snpeff_cache invalid. Make sure there is a directory named ${snpeff_cache_dir} in ${params.snpeff_cache}.\nhttps://nf-co.re/sarek/dev/usage#how-to-customise-snpeff-and-vep-annotation")
Copy link
Contributor

Choose a reason for hiding this comment

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

for the release we need to check all the error message point to the release docs. I think there are also a couple left in other error messages

maxulysse
maxulysse commented Sep 28, 2023
View reviewed changes
docs/usage.md Outdated Show resolved Hide resolved
@maxulysse maxulysse merged commit 4cb2c2a into nf-core:dev Sep 28, 2023
20 checks passed
@maxulysse maxulysse deleted the annotation_cache_docs branch September 28, 2023 14:01
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@FriederikeHanssen FriederikeHanssen FriederikeHanssen 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.
2 participants
@maxulysse @FriederikeHanssen