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Add parameter freyja_depthcutoff #412

Merged
merged 4 commits into from
Jan 25, 2024
Merged

Add parameter freyja_depthcutoff #412

merged 4 commits into from
Jan 25, 2024

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Joon-Klaps
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PR checklist

Solves issue #405

Freyja is throws a known error if it deals with samples of low coverage. It got fixed in this PR andersen-lab/Freyja#145 by including the option --depthcutoff.

  • 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).

@Joon-Klaps Joon-Klaps changed the base branch from master to dev January 17, 2024 12:40
@nf-core nf-core deleted a comment from github-actions bot Jan 17, 2024
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github-actions bot commented Jan 17, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 66d2cf1

+| ✅ 150 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ 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 2.11.1
  • Run at 2024-01-25 10:56:36

@Joon-Klaps
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@nf-core-bot fix linting

@svarona
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svarona commented Jan 24, 2024

Maybe you should add the changes to the CHANGELOG.md?

@Joon-Klaps
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Maybe you should add the changes to the CHANGELOG.md?

Forgot, I'll do my other PR as well.

svarona
svarona reviewed Jan 25, 2024
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CHANGELOG.md
| `--freyja_db_name` | |
| `--freyja_barcodes` | |
| `--freyja_lineages` | |
| `--freyja_depthcutoff` | |
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I think --freyja_depthcutoff should go in the new parameter column?

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I thought so too 😅 but given that the previous PR, introducing freyja had its variables in the old column I putted it there.

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Okay then everything looks good to me!

@Joon-Klaps Joon-Klaps merged commit de5146a into dev Jan 25, 2024
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@Joon-Klaps Joon-Klaps deleted the 405-adding-depthcutoff-freyja branch January 25, 2024 16:13
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@svarona svarona svarona approved these changes

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@Joon-Klaps @svarona @nf-core-bot