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add insertsizemetrics to QC workflow #408

Merged
merged 11 commits into from
Oct 20, 2023
Merged

add insertsizemetrics to QC workflow #408

merged 11 commits into from
Oct 20, 2023

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rannick
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@rannick rannick commented Sep 25, 2023 •
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add insertsizemetrics to QC workflow

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 self-assigned this Sep 25, 2023
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github-actions bot commented Sep 25, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3e4165c

+| ✅ 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 2023-10-20 14:08:44

@rannick rannick marked this pull request as ready for review September 29, 2023 13:43
@rannick rannick requested review from peterpru and fevac and removed request for peterpru October 2, 2023 10:46
@rannick rannick requested a review from peterpru October 2, 2023 10:46
fevac
fevac approved these changes Oct 2, 2023
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Looks good! Just few things:

  1. Have we tested a small case with this? Good be good to know that it works as intended and how long this steps takes
  2. Is this output integrated and included by the multiqc step?

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rannick commented Oct 20, 2023

  1. All tested! The time it takes seems to be similar or less than the other picard metrics: PICARD_COLLECTRNASEQMETRICS
  2. Yes it is integrated

@rannick rannick merged commit 6a18471 into dev Oct 20, 2023
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@rannick rannick deleted the collectinsertsizemetrics branch October 20, 2023 14:21
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@fevac fevac fevac approved these changes

@peterpru peterpru Awaiting requested review from peterpru

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