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

Apply samtools fixmate after ivar trim #396

Open
wants to merge 4 commits into
base: dev
Choose a base branch
from
Open

Apply samtools fixmate after ivar trim #396

wants to merge 4 commits into from

Conversation

wutron
Copy link

@wutron wutron commented Sep 21, 2023 •
edited
Loading

Apply samtools fixmate to fix template length after primer trimming. Not necessary for viralrecon per se but cleans up alignment if user wants to use other tools downstream, e.g. samtools ampliconstats.
https://github.com/samtools/samtools/blob/007d83e8b63737d8a08060723a41eba4a1df3f7a/amplicon_stats.c#L583

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/viralrecon 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>).
  • 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).

@github-actions
Copy link

github-actions bot commented Oct 2, 2023 •
edited
Loading

nf-core lint overall result: Failed ❌

Posted for pipeline commit 0663ed2

+| ✅ 145 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   5 tests had warnings |!
-| ❌   3 tests failed       |-

❌ Test failures:

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: lib/WorkflowViralrecon.groovy
  • 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
  • system_exit - System.exit in nanopore.nf: System.exit(1) [line 237]

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-16 14:51:24

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.
1 participant
@wutron