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Apply samtools fixmate after ivar trim #396

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@wutron wutron commented Sep 21, 2023 •
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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).

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github-actions bot commented Oct 2, 2023 •
edited

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

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