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

Longread only functionality #718

Open
wants to merge 18 commits into
base: dev
Choose a base branch
from
Open

Longread only functionality #718

wants to merge 18 commits into from

Conversation

muabnezor
Copy link
Contributor

This PR adds long-read only functionality to mag.

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).

@muabnezor muabnezor added the WIP Work in progress label Nov 28, 2024
@github-actions GitHub Actions
Copy link

This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @muabnezor,

It looks like this pull-request is has been made against the muabnezor/mag master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the muabnezor/mag dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@muabnezor muabnezor changed the base branch from master to dev November 28, 2024 12:29
d4straub
d4straub reviewed Nov 28, 2024
View reviewed changes
Copy link
Collaborator

@d4straub d4straub left a comment

Choose a reason for hiding this comment

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

I only had a short look, sorry, but I just wanted to express my gratitude that you tackle long read assembly!

nextflow.config
@@ -53,6 +53,7 @@ params {
min_length_unbinned_contigs = 1000000
max_unbinned_contigs = 100
skip_prokka = false
longread_percentidentity = 90
Copy link
Collaborator

Choose a reason for hiding this comment

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

thats missing in the nextflow_schema.json, right?

prototaxites
prototaxites reviewed Nov 28, 2024
View reviewed changes
conf/modules.config Outdated
@@ -551,6 +620,7 @@ process {
}

withName: METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS {
ext.args = { meta.assembler in ['FLYE', 'METAMDBG'] ? "--percentIdentity ${params.longred_percentidentity}" : '' }
Copy link
Contributor

Choose a reason for hiding this comment

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

typo: longred_percentidentity

Copy link
Contributor Author

Choose a reason for hiding this comment

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

Whoops, thank you!

@muabnezor
Copy link
Contributor Author

I only had a short look, sorry, but I just wanted to express my gratitude that you tackle long read assembly!

My pleasure hehe. Still WIP. I have to tidy up the code and run some validation on real data, but we're getting there!

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

@d4straub d4straub d4straub left review comments

@prototaxites prototaxites prototaxites left review comments

@jfy133 jfy133 Awaiting requested review from jfy133

At least 1 approving review is required to merge this pull request.

Assignees
No one assigned
Labels
WIP Work in progress
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
3 participants
@muabnezor @prototaxites @d4straub