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

Update SPAdes module to official nf-core and version bump #666

Open
wants to merge 5 commits into
base: dev
Choose a base branch
from
Open

Update SPAdes module to official nf-core and version bump #666

wants to merge 5 commits into from

Conversation

jfy133
Copy link
Member

@jfy133 jfy133 commented Sep 9, 2024 •
edited
Loading

TODO:

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>).
  • 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 linked an issue Sep 9, 2024 that may be closed by this pull request
Update metaspades to 4.0.0 #640
Open
@github-actions GitHub Actions
Copy link

github-actions bot commented Sep 9, 2024 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 89f98e2

+| ✅ 306 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   5 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 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!

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-09-10 14:36:01

@jfy133
Copy link
Member Author

jfy133 commented Sep 10, 2024

Need to check other downstreeam files to make sure if there is an issue, however it seems that the original SPADES(HYBIRD) modules exported the the main scaffolds as uncompressed for downstream.( even though it also exported a version as compressed).

I think I will need to add an additional GUNZIP module after the assembly for safety...

@jfy133
Copy link
Member Author

jfy133 commented Sep 12, 2024 •
edited
Loading

Added the GUNZIP module actually does somthing similar to pre-assemblies, but then local MEGAHIT module also exports uncompressed files... so I guess time to update this too

But I need to udpate the MEGAHIT module to support co-assemblies (basically reads.join()

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

Update metaspades to 4.0.0
1 participant
@jfy133