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 macrel faa input #242

Merged
merged 10 commits into from
Apr 14, 2023
Merged

fix macrel faa input #242

merged 10 commits into from
Apr 14, 2023

Conversation

Darcy220606
Copy link
Contributor

@Darcy220606 Darcy220606 commented Mar 8, 2023 •
edited
Loading

This PR fixes the MACREL input issue in the pipeline amp workflow. The issue was that MACREL module is currently using fna and running its own annoations therfore when MACREl is run alone in the pipeline AMPCOMBI was not activated as it was missing one of its input = faa. To fix this i added the faa generated by MACREl into the summary channel. This closes issue #241
MACREL alse needs updating in FUNCSCAN/MODULES an issue #3001 was also created.

  • 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/funcscan 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 Mar 8, 2023 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 6b34f55

+| ✅ 157 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline

✅ Tests passed:

Run details

  • nf-core/tools version 2.7.2
  • Run at 2023-04-13 17:17:17

@Darcy220606 Darcy220606 requested review from a team and removed request for jfy133, louperelo and jasmezz March 8, 2023 17:17
@Darcy220606 Darcy220606 linked an issue Mar 10, 2023 that may be closed by this pull request
AMPcombi does not execute when only MACREL #241
Closed
louperelo
louperelo approved these changes Mar 15, 2023
View reviewed changes
Copy link
Contributor

@louperelo louperelo left a comment

Choose a reason for hiding this comment

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

looks good to me
Took me a bit to understand how AMPcombi could deal with a channel if it contains two faa files, but realised it always considers the one on position 2 ...

@jfy133
Copy link
Member

jfy133 commented Mar 17, 2023

@Darcy220606 please just check locally it works correctly now I've resolved the merge conflict, then you can merge :)

jfy133
jfy133 reviewed Mar 29, 2023
View reviewed changes
subworkflows/local/amp.nf Outdated Show resolved Hide resolved
louperelo
louperelo reviewed Apr 6, 2023
View reviewed changes
Copy link
Contributor

@louperelo louperelo left a comment

Choose a reason for hiding this comment

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

Continues looking good.

subworkflows/local/amp.nf Show resolved Hide resolved
@Darcy220606 Darcy220606 merged commit 6c6ab7d into nf-core:dev Apr 14, 2023
This was referenced Apr 20, 2023
Closed
Merged
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@louperelo louperelo louperelo approved these changes

@jfy133 jfy133 jfy133 left review comments

Assignees

@Darcy220606 Darcy220606

Labels
None yet
Projects
No open projects
nf-core Hackathon March 2023
Status: Done
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

AMPcombi does not execute when only MACREL
4 participants
@Darcy220606 @jfy133 @louperelo @jasmezz