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Inclusion of a working ion annotator #238

Merged
merged 19 commits into from
Nov 17, 2022
Merged

Inclusion of a working ion annotator #238

merged 19 commits into from
Nov 17, 2022

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marissaDubbelaar
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@marissaDubbelaar marissaDubbelaar commented Nov 17, 2022 •
edited

  • #229 Add ion annotation feature requested in #220
  • #235 Add the annotate_ions parameter to enable/disable the ion annotation feature (default is true)
  • Fix for an inconsistent mzml channel issue

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/mhcquant 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 Nov 17, 2022 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0ba17f2

+| ✅ 156 tests passed       |+
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • 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 passed:

Run details

  • nf-core/tools version 2.6
  • Run at 2022-11-17 13:05:26

jonasscheid
jonasscheid requested changes Nov 17, 2022
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@jonasscheid jonasscheid left a comment

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minor typos , else LGTM

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marissaDubbelaar and others added 3 commits November 17, 2022 14:03
@marissaDubbelaar @jonasscheid
Update CHANGELOG.md
d205136 
Co-authored-by: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com>
@marissaDubbelaar @jonasscheid
Update conf/modules.config
07fef27 
Co-authored-by: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com>
@marissaDubbelaar @jonasscheid
Update nextflow_schema.json
0ba17f2 
Co-authored-by: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com>
@marissaDubbelaar marissaDubbelaar merged commit 9cb6d46 into nf-core:dev Nov 17, 2022
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@jonasscheid jonasscheid jonasscheid approved these changes

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@marissaDubbelaar @jonasscheid