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add extra options for fusioninspector #426

Merged
merged 7 commits into from
Oct 25, 2023
Merged

add extra options for fusioninspector #426

merged 7 commits into from
Oct 25, 2023

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rannick
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@rannick rannick commented Oct 23, 2023 •
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Adding options --max_sensitivity --max_mate_dist 10000000 --annotate --examine_coding_effect to fusioninspector to collect more data and keep FFPM calculation, which did not work with extreme_sensistivity

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/rnafusion 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).

@rannick rannick added the WIP Work in progress label Oct 23, 2023
@rannick rannick self-assigned this Oct 23, 2023
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github-actions bot commented Oct 23, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit cc9e67b

+| ✅ 158 tests passed       |+
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • pipeline_todos - TODO string in WorkflowRnafusion.groovy: Optionally add in-text citation tools to this list.

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-25 09:18:39

@rannick rannick added waiting-for-review and removed WIP Work in progress labels Oct 25, 2023
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rannick commented Oct 25, 2023

Test passed

ivadym
ivadym approved these changes Oct 25, 2023
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👍

@rannick rannick merged commit 388d917 into dev Oct 25, 2023
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@rannick rannick deleted the fusioninspector_extra_options branch October 25, 2023 09:36
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@ivadym ivadym ivadym approved these changes

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