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Patch Release 2.2.2#621

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jfy133 merged 74 commits intomasterfrom
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Dec 9, 2020
Merged

Patch Release 2.2.2#621
jfy133 merged 74 commits intomasterfrom
dev

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@jfy133
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@jfy133 jfy133 commented Dec 2, 2020

nf-core/eager pull request

This PR is for release of the 2.2.2 patch.

This most important includes:

  • Fixes for AdapterRemoval (to allow for correct compatibilty with dedup)
  • Drops requirement for user to supply own GATK 3.5 jar, now it has been retroactively re-licensed
  • nf-core Template update to 1.12.

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 necessary, also make a PR on the nf-core/eager branch on the nf-core/test-datasets repo
  • Ensure the test suite passes (nextflow run . -profile test,docker --paired_end).
  • Make sure your code lints (nf-core lint .).
  • Documentation in docs is updated
  • CHANGELOG.md is updated
  • README.md is updated

Learn more about contributing: CONTRIBUTING.md

jfy133 and others added 30 commits October 21, 2020 08:57
Get AWS last minute fixes
Important! Template update for nf-core/tools v1.11
Added link to 1240k bedfile. Typo.
fix aws full test profiles
Bump runtimes for human stresstesting
Final chance...
@jfy133 jfy133 requested a review from apeltzer December 2, 2020 11:04
@jfy133 jfy133 requested a review from TCLamnidis December 2, 2020 11:05
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@apeltzer apeltzer left a comment

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LGTM

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@ewels ewels left a comment

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The metro map is so cool! 🤩

Generally looks good, except the big one that all parameter documentation should be stripped from usage.md.

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@jfy133 jfy133 requested a review from ewels December 8, 2020 08:32
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@ewels ewels left a comment

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Ace! Couple of super tiny niggles but otherwise good to go.

As discussed on Slack, could be nice to move the very long --help text back to usage.md (sorry 👀 ) but that's an optional extra. See atacseq dev for an example of where this has been done in another pipeline: https://nf-co.re/atacseq/dev/usage

Comment thread nextflow_schema.json Outdated
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@jfy133 jfy133 merged commit 85e2e32 into master Dec 9, 2020
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9 participants