Skip to content

Re-add contigs vs scaffolds metaSPAdes selection#979

Open
jfy133 wants to merge 1 commit intodevfrom
readd-spades-contigs-option
Open

Re-add contigs vs scaffolds metaSPAdes selection#979
jfy133 wants to merge 1 commit intodevfrom
readd-spades-contigs-option

Conversation

@jfy133
Copy link
Member

@jfy133 jfy133 commented Feb 9, 2026 •
edited
Loading

Re-adds functionality added in #745

Was accidently lost during the re-factoring of the assembly steps to workflows due to concurent development.

Reported https://nfcore.slack.com/archives/CE9MS66BS/p1770452516999219

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 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).

@nf-core-bot
Copy link
Member

nf-core-bot commented Feb 9, 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.

@jfy133 jfy133 marked this pull request as ready for review February 9, 2026 08:38
@github-actions
Copy link

github-actions bot commented Feb 9, 2026

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit c00d519

+| ✅ 383 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   6 tests had warnings |!
Details

❗ 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 methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2026-02-09 08:40:20

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@prototaxites prototaxites prototaxites approved these changes

@d4straub d4straub Awaiting requested review from d4straub d4straub is a code owner

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

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

Assignees

No one assigned

Labels

size/xs

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

3 participants

@jfy133 @nf-core-bot @prototaxites