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Updates #35

Merged
merged 18 commits into from
Sep 17, 2019
Merged

Updates #35

merged 18 commits into from
Sep 17, 2019

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maxulysse
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@maxulysse maxulysse commented Sep 15, 2019 •
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  • Building indexes is now done in main.nf
  • Use tabix instead of IGVtools to build vcf indexes
  • Remove IGVtools
  • Clean up environment.yml file
  • Building indexes from nf-core/test-datasets:sarek
  • Remove building indexes from build.nf script
  • Remove helper script build_reference.sh
  • build.nf script only download cache, so renamed to downloadcache.nf
  • Refactor references handling
  • Remove referenceMap and defineReferenceMap() and use Channel values instead
  • Remove Mutect2 from MULTIPLE test

Many thanks to contributing to nf-core/sarek!

Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs).

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/sarek branch on the nf-core/test-datasets repo
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • 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: https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md

@maxulysse
Update tools
107a0f3 
- `control-freec` from `11.4` to `11.5`
- `ensembl-vep` from `95.2` to `97.3`
- `freebayes` from `1.2.0` to `1.3.1`
- `gatk4` from `4.1.2.0` to `4.1.3.0`
- `igvtools` from `2.3.93` to `2.5.3`
- `manta` from `1.5.0` to `1.6.0`
- `qualimap` from `2.2.2b` to `2.2.2c`
- `vcfanno` from `0.3.1` to `0.3.2`
@maxulysse
update CHANGELOG
2c71f7c
@maxulysse
update files
497c00e
@maxulysse
rename script
a1a56f6
@maxulysse
Merge remote-tracking branch 'upstream/dev' into Updates
542d4d1
@maxulysse
code polishing
f8d78f3
@maxulysse
revert updates
55ffad3
@maxulysse
revert updates
9930681
@maxulysse
update docs
ae2f03e
@maxulysse
add comments to params
2eb4f6e
@maxulysse
remove Mutect2 from MULTIPLE
574790a
@maxulysse
more code polishing
9d780da
@maxulysse
update CHANGELOG
6c69699
@maxulysse
more code polishing
87adf67
maxulysse
maxulysse commented Sep 17, 2019
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@maxulysse maxulysse mentioned this pull request Sep 17, 2019
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@maxulysse maxulysse self-assigned this Sep 17, 2019
@maxulysse maxulysse requested a review from a team September 17, 2019 12:48
@maxulysse
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⚠️ This PR: nf-core/test-datasets#74 needs to be merged before, and the change suggested need to be applied before merging this PR.

apeltzer
apeltzer requested changes Sep 17, 2019
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Looks good to me, I can't however commit your suggested changes due to permissions @maxulysse - maybe check this yourself!

@maxulysse
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OK, I just accepted the changes

@apeltzer
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Then you should be ready to go once this passed CI 👍

PR to test-datasets has been merged, so this should now run through smoothly 🎉

@maxulysse
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That's exactly what I was writing ;-)

ewels
ewels reviewed Sep 17, 2019
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main.nf
// Handle deprecation
// Default value for params

// Set deprecated params to null
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Can you put all of this params initialisation into the config files? Unless it's a complex case requiring logic (eg. as we do with params.genome and the references), I usually try to put all params initialisation into the base.config. Keeps the main script a lot cleaner.

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I'll do that in the PR for the release, I'll prefer to merge this one as soon as possible, as it's breaking stuff for now

@apeltzer apeltzer merged commit d98640c into nf-core:dev Sep 17, 2019
@maxulysse maxulysse deleted the Updates branch September 18, 2019 07:32
@maxulysse maxulysse mentioned this pull request Sep 18, 2019
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@ewels ewels ewels left review comments

@apeltzer apeltzer apeltzer approved these changes

@szilvajuhos szilvajuhos Awaiting requested review from szilvajuhos

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@maxulysse @apeltzer @ewels