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PR for 2.3 release #649

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jfy133 merged 50 commits intomasterfrom
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Jan 11, 2021
Merged

PR for 2.3 release #649
jfy133 merged 50 commits intomasterfrom
dev

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@jfy133
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@jfy133 jfy133 commented Jan 4, 2021

This PR is for 2.3 - "Aalen".

It includes a couple of minor bug fixes, and also additional functionality request by reviewers of the nf-core manuscript.

Functionality includes

  • Low-sequence complexity read filtering prior metagenomic screening
  • mapDamage rescaling of BAM files

Fixed issues

  • DeDup nullPointerException fix (version bump)
  • Fixed AWS stress test a bit more
  • Fixed some mistakes in schema regarding dropdowns
  • Fixed a (semi-)major bug where filtering options using circularmapper was flipped

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 - add to the software_versions process and a regex to scrape_software_versions.py
  • 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/eager 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).

jfy133 and others added 30 commits December 9, 2020 09:09
Post release dev version bump
Improve memory and error handling of qualimap
Co-authored-by: Thiseas C. Lamnidis <thisseass@gmail.com>
Co-authored-by: Thiseas C. Lamnidis <thisseass@gmail.com>
Add Damage rescaling functionality
Comment thread README.md Outdated
Comment thread bin/scrape_software_versions.py
Comment thread main.nf
Comment thread main.nf
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@maxulysse maxulysse left a comment

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Looks good to me ;-)

Co-authored-by: Maxime Garcia <max.u.garcia@gmail.com>
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@apeltzer apeltzer left a comment

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LGTM :-)

@jfy133 jfy133 merged commit 0bc87f3 into master Jan 11, 2021
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5 participants