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

fix(fusionreport) set html as optional #380

Merged
merged 6 commits into from
Aug 25, 2023
Merged

fix(fusionreport) set html as optional #380

merged 6 commits into from
Aug 25, 2023

Conversation

fevac
Copy link
Contributor

@fevac fevac commented Aug 21, 2023 •
edited
Loading

Part of: #376

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/rnafusion 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

This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @fevac,

It looks like this pull-request is has been made against the nf-core/rnafusion master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the nf-core/rnafusion dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@fevac fevac changed the base branch from master to dev August 21, 2023 13:40
@github-actions
Copy link

github-actions bot commented Aug 21, 2023 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5c84661

+| ✅ 156 tests passed       |+
!| ❗   2 tests had warnings |!

❗ Test warnings:

✅ Tests passed:

Run details

  • nf-core/tools version 2.7.2
  • Run at 2023-08-25 07:23:21

@fevac
Copy link
Contributor Author

fevac commented Aug 22, 2023

@rannick as we thought the error propagates and fails in fusioninspector

With error message:
No fusions listed in input file: <case_id>.fusionreport.tsv, exiting gracefully.

Looking into it

@fevac
Copy link
Contributor Author

fevac commented Aug 22, 2023

Actually I'm not sure how we want to handle this, if empty files or handling the error. Let's talk tomorrow

@rannick
Copy link
Collaborator

rannick commented Aug 23, 2023

I would limit the change to fusionreport and implement a logical gate in case fusionreport output is empty in another PR, i.e. keep fusioninspector unchanged. Does that make sense to you?

@efgstone
Copy link

Hi @fevac - I'm interested to hear how you are getting on with this fix as the same issue is currently preventing me from using this workflow - is there anything I can work with you on?

@fevac
Copy link
Contributor Author

fevac commented Aug 24, 2023

Hi @fevac - I'm interested to hear how you are getting on with this fix as the same issue is currently preventing me from using this workflow - is there anything I can work with you on?

The plan is to do what @rannick suggested above: so implementing a logical switch in a different PR. I have not started yet so feel free to start if you have the time. Not sure if @rannick might have time or has been looking into it

@rannick rannick marked this pull request as ready for review August 25, 2023 06:57
@rannick
Copy link
Collaborator

rannick commented Aug 25, 2023

@efgstone @fevac yes, I am looking into it. Currently working on merging the template 2.9, which turned out more tricky than anticipated but that is right next for me. Expect an at least partial patch (no fusion-report reference fix) mid-next week I would say

@fevac fevac merged commit ea2b723 into dev Aug 25, 2023
6 checks passed
@rannick rannick deleted the fix_fusionreport_optional_html branch August 25, 2023 08:12
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@rannick rannick rannick 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.
3 participants
@fevac @rannick @efgstone