Thanks to visit codestin.com
Credit goes to github.com

Skip to content

Comments

Longread hostremoval fixes#683

Merged
jfy133 merged 3 commits intodevfrom
longread-hostremoval-fixes
Feb 11, 2026
Merged

Longread hostremoval fixes#683
jfy133 merged 3 commits intodevfrom
longread-hostremoval-fixes

Conversation

@jfy133
Copy link
Member

@jfy133 jfy133 commented Feb 11, 2026

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/taxprofiler branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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).

jfy133
jfy133 commented Feb 11, 2026
View reviewed changes
@nf-core-bot
Copy link
Member

nf-core-bot commented Feb 11, 2026

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

@github-actions
Copy link

github-actions bot commented Feb 11, 2026 •
edited
Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 755a5db

+| ✅ 290 tests passed       |+
!| ❗  18 tests had warnings |!
Details

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • local_component_structure - kraken2_standard_report.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - krona_cleanup.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - visualization_krona.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - shortread_complexityfiltering.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - profiling.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - longread_hostremoval.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - longread_preprocessing.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - shortread_fastp.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - longread_adapterremoval.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - standardisation_profiles.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - shortread_preprocessing.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - shortread_adapterremoval.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - longread_filtering.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - nonpareil.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - shortread_hostremoval.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2026-02-11 11:08:01

sofstam
sofstam reviewed Feb 11, 2026
View reviewed changes
Copy link
Collaborator

@sofstam sofstam left a comment

Choose a reason for hiding this comment

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

Which issue does this PR close?

@jfy133
Copy link
Member Author

jfy133 commented Feb 11, 2026 •
edited
Loading

It doesn't 😆

Was trying to debug a users report on Slack, but couldn't even get to reproducing it because I was hitting other issues which I'm fixing here...

sofstam
sofstam approved these changes Feb 11, 2026
View reviewed changes
Copy link
Collaborator

@sofstam sofstam 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 merged commit 8997d95 into dev Feb 11, 2026
11 checks passed
@jfy133 jfy133 deleted the longread-hostremoval-fixes branch February 11, 2026 13:13
@jfy133 jfy133 restored the longread-hostremoval-fixes branch February 11, 2026 13:13
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@sofstam sofstam sofstam approved these changes

@LilyAnderssonLee LilyAnderssonLee Awaiting requested review from LilyAnderssonLee LilyAnderssonLee is a code owner

Assignees

No one assigned

Labels

size/s

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

3 participants

@jfy133 @nf-core-bot @sofstam