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Add --skip_prodigal#241

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AntoniaBeller merged 6 commits intonf-core:devfrom
AntoniaBeller:skip_prodigal
Oct 29, 2021
Merged

Add --skip_prodigal#241
AntoniaBeller merged 6 commits intonf-core:devfrom
AntoniaBeller:skip_prodigal

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@AntoniaBeller AntoniaBeller commented Oct 29, 2021 •
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Added the option --skip_prodigal, so that gene prediction can be skipped when not necessary.

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).
  • 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 29, 2021 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit deb8358

+| ✅ 136 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   1 tests had warnings |!
Details

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version mentioned in Quick Start section.

❔ Tests ignored:

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

✅ Tests passed:

Run details

  • nf-core/tools version 2.1
  • Run at 2021-10-29 09:08:30

d4straub
d4straub approved these changes Oct 29, 2021
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I have just minor comments, looks good!

Comment thread CHANGELOG.md Outdated
Comment thread nextflow.config
AntoniaBeller and others added 2 commits October 29, 2021 11:05
@AntoniaBeller @d4straub
Update CHANGELOG.md
4df589b 
Co-authored-by: Daniel Straub <[email protected]>
@AntoniaBeller @d4straub
Update nextflow.config
deb8358 
Co-authored-by: Daniel Straub <[email protected]>
@AntoniaBeller AntoniaBeller merged commit 554caee into nf-core:dev Oct 29, 2021
@AntoniaBeller AntoniaBeller deleted the skip_prodigal branch October 29, 2021 10:26
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@d4straub d4straub d4straub approved these changes

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@AntoniaBeller @d4straub