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Patch Release: 2.3.3 #720

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Merged
jfy133 merged 67 commits into from
Apr 8, 2021
Merged

Patch Release: 2.3.3 #720

jfy133 merged 67 commits into from
Apr 8, 2021

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@jfy133 jfy133 commented Apr 6, 2021

Release for patch 2.3.3

Added

  • #349 - Added option enabling platypus formatted output of pmdtools misincorporation frequencies.

Fixed

  • #719 - Fix filename for bam output of mapdamage_rescaling
  • #707 - Fix typo in UnifiedGenotyper IndelRealigner command
  • Fixed some Java tools not following process memory specifications
  • Updated template to nf-core/tools 1.13.2
  • #711 - Fix conditional execution preventing multivcfanalyze to run
  • #714 - Fixes bug in nuc contamination by upgrading to latest MultiQC v1.10.1 bugfix release

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 March 16, 2021 16:45
@jfy133
Post-release version bump
b625e98
@jfy133
Update changelog post-release
150b0b0
@jfy133
Merge pull request #704 from jfy133/dev
3d83b42 
Post release version bump
@nf-core-bot
Template update for nf-core/tools version 1.13
197fb1a
@nf-core-bot
Template update for nf-core/tools version 1.13.1
574bab5
@IdoBar
Fix typo in UnifiedGenotyper IndelRealigner command
1591207 
Changed {samplenane} to {samplename} (line 2337)
@IdoBar
Update CHANGELOG.md
a810c45
@IdoBar
Update CHANGELOG.md
14615f5
@jfy133
Merge branch 'dev' into patch-5
1a2f3ca
@jfy133
Merge pull request #707 from IdoBar/patch-5
7296290 
Fix typo in UnifiedGenotyper IndelRealigner command
@TCLamnidis
Added pmdtools_platypus parameter, to pmdtools process.
614b196
@TCLamnidis
Added pmdtools_platypus parameter
92be525
@TCLamnidis
Added params.pmdtools_platypus
3815636
@TCLamnidis
Formatting changes for consistency.
9e63991
@nf-core-bot
Template update for nf-core/tools version 1.13.2
6b4e021
@jfy133
Merge branch 'dev' into nf-core-template-merge-1.13.2
b906bde
@jfy133
Linting fixes
9741804
@jfy133
Resolve first set of linting issues
ecbeb38
@jfy133
Further fixes from merging issues
ac547f2
@jfy133
Use nf-core auto-fix
c37c854
@maxibor
fix condition preventing to run multivcfanalyzer
b1a132d
@maxibor
update gatk_hc_out_mode
6328dc4
@jfy133
Fixed legacy parameters and cleaned up WARN due to our non-default ig…
372ff0a 
…enomes param
@jfy133
Merge pull request #709 from nf-core/nf-core-template-merge-1.13.2
9d451bd 
Important! Template update for nf-core/tools v1.13.2
@TCLamnidis
Merge branch 'dev' into pmd-tools-extention
ded5972
@TCLamnidis
Merge confliict resolved
5acf68c
@jfy133
Add missing Xmx for Java tools
c23e777
@TCLamnidis
linting
59a40b1
@maxibor
Merge branch 'dev' of github.com:nf-core/eager into dev
d11de6a
@jfy133
Update main.nf
e45eeb2
TCLamnidis
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The linter assumes any - at the start of a line is a markdown bullet. That should not be applied within code blocks...
usage.md is in need of some TLC (many more instances than I suggested changes for). Preferably, we should fix the linter, then checkout and re-lint usage (assuming all changes are linting related).

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github-actions bot commented Apr 7, 2021

Markdown linting is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

  • Install markdownlint-cli
  • Fix the markdown errors
    • Automatically: markdownlint . --config .github/markdownlint.yml --fix
    • Manually resolve anything left from markdownlint . --config .github/markdownlint.yml

Once you push these changes the test should pass, and you can hide this comment 👍

We highly recommend setting up markdownlint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!

@jfy133 jfy133 requested review from TCLamnidis and apeltzer April 7, 2021 18:34
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Happy for merging after the small linting typos are corrected. In my suggestions I changed - for — for parenthetical sentences, which the linters should leave alone in the future. 🤞

@jfy133 @TCLamnidis
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Co-authored-by: Thiseas C. Lamnidis <[email protected]>
@jfy133 jfy133 merged commit ad8e41a into master Apr 8, 2021
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@apeltzer apeltzer apeltzer approved these changes

@TCLamnidis TCLamnidis TCLamnidis approved these changes

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@jfy133 @apeltzer @TCLamnidis @nf-core-bot @IdoBar @maxibor