Skip to content

bwa should use -Y and not -M#644

Merged
maxulysse merged 3 commits intonf-core:devfrom
FriederikeHanssen:bwa_args
Jul 17, 2022
Merged

bwa should use -Y and not -M#644
maxulysse merged 3 commits intonf-core:devfrom
FriederikeHanssen:bwa_args

Conversation

@FriederikeHanssen
Copy link
Copy Markdown
Contributor

@FriederikeHanssen FriederikeHanssen commented Jul 17, 2022 •
edited
Loading

close #101

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 - add to the software_versions process and a regex to scrape_software_versions.py
    • 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/sarek 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).
  • 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).

@maxulysse
Copy link
Copy Markdown
Member

maxulysse commented Jul 17, 2022

Should we look into similar settings fro dragmap?

@github-actions
Copy link
Copy Markdown

github-actions Bot commented Jul 17, 2022 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f5f49ea

+| ✅ 145 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!
Details

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-07-17 10:38:19

@FriederikeHanssen
Copy link
Copy Markdown
Contributor Author

FriederikeHanssen commented Jul 17, 2022

Should we look into similar settings fro dragmap?

yes, good point

@FriederikeHanssen
Copy link
Copy Markdown
Contributor Author

FriederikeHanssen commented Jul 17, 2022

the command used for dragmap is the most basic one according to the docs. Couldn't find something simialr as for the bwa yet. Maybe for now the basic command is fine and we keep an eye on the developments there

@maxulysse maxulysse merged commit d2388d1 into nf-core:dev Jul 17, 2022
@FriederikeHanssen FriederikeHanssen mentioned this pull request Jul 17, 2022
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@maxulysse maxulysse maxulysse approved these changes

Assignees

No one assigned

Labels

None yet

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

2 participants

@FriederikeHanssen @maxulysse
⚡