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 missing GUNC overwriting #514 #515

Merged
merged 6 commits into from
Sep 27, 2023
Merged

Fix missing GUNC overwriting #514 #515

merged 6 commits into from
Sep 27, 2023

Conversation

jfy133
Copy link
Member

@jfy133 jfy133 commented Sep 26, 2023

Wait until #511 is merged! Then test before requesting review!

closes #502 to stop GUNC overwriting otuput directories when running with domain classification

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/mag 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 Sep 26, 2023 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f9691cf

+| ✅ 158 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file [TODO: try and test using for --host_fasta and --host_genome]
  • pipeline_todos - TODO string in WorkflowMag.groovy: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-09-27 14:50:14

@jfy133 jfy133 requested a review from maxibor September 26, 2023 17:25
@jfy133 jfy133 changed the title [DO NOT MERGE] Fix missing GUNC overwriting #514 Fix missing GUNC overwriting #514 Sep 27, 2023
jfy133
jfy133 commented Sep 27, 2023
View reviewed changes
docs/output.md Outdated Show resolved Hide resolved
@jfy133
Copy link
Member Author

jfy133 commented Sep 27, 2023

I confirm this works:

image

nextflow run ../main.nf -profile singularity,test --outdir ./results --skip_concoct false --skip_spadeshybrid --skip_prokka --skip_prodigal --run_gunc --bin_domain_classification

prototaxites
prototaxites approved these changes Sep 27, 2023
View reviewed changes
Copy link
Contributor

@prototaxites prototaxites left a comment

Choose a reason for hiding this comment

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

LGTM 👍

CarsonJM
CarsonJM approved these changes Sep 27, 2023
View reviewed changes
Copy link
Contributor

@CarsonJM CarsonJM 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!

@jfy133 jfy133 merged commit e8316ab into dev Sep 27, 2023
15 checks passed
@jfy133 jfy133 deleted the fix-gunc-overwriting branch October 3, 2023 13:57
@jfy133 jfy133 mentioned this pull request Oct 9, 2023
Merged
10 tasks
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@CarsonJM CarsonJM CarsonJM approved these changes

@prototaxites prototaxites prototaxites approved these changes

@maxibor maxibor Awaiting requested review from maxibor

@d4straub d4straub Awaiting requested review from d4straub

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
@jfy133 @prototaxites @CarsonJM