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Update genome commandline parameter#344

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alexhbnr merged 1 commit intonf-core:devfrom
alexhbnr:fix_doc_genome
Oct 20, 2022
Merged

Update genome commandline parameter#344
alexhbnr merged 1 commit intonf-core:devfrom
alexhbnr:fix_doc_genome

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@alexhbnr alexhbnr commented Oct 17, 2022

This PR fixes the minimal code example to run the pipeline and updates the parameter --genome to --host_genome.

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 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 17, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4b70648

+| ✅ 156 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   1 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.6
  • Run at 2022-10-17 14:24:38

d4straub
d4straub approved these changes Oct 19, 2022
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Thanks, LGTM!

@alexhbnr alexhbnr merged commit 2e05bd0 into nf-core:dev Oct 20, 2022
@alexhbnr alexhbnr deleted the fix_doc_genome branch October 20, 2022 17:59
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@d4straub d4straub d4straub approved these changes

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@alexhbnr @d4straub