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2.6.1 #222

Merged
merged 26 commits into from
Jun 23, 2020
Merged

2.6.1 #222

merged 26 commits into from
Jun 23, 2020

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maxulysse
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nf-core/sarek pull request

Many thanks for 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: CONTRIBUTING.md

maxulysse and others added 23 commits May 24, 2020 12:20
@maxulysse
bump version 3.0dev
6da920a
@maxulysse
Merge pull request nf-core#208 from MaxUlysse/dev
25dd584 
Getting dev up to date
@maxulysse
extend timeout for pushing to dockerhub
60853a2
@maxulysse
update CHANGELOG
ad232f0
@maxulysse
Merge pull request nf-core#211 from MaxUlysse/dev
c90c8e6 
extend timeout for pushing to dockerhub
@maxulysse
no aws test on forks
cd3ed51
@maxulysse
update CHANGELOG
dcce12f
@maxulysse
update CHANGELOG
6af94f7
@maxulysse
Merge pull request nf-core#212 from MaxUlysse/no_aws_test_on_forks
ca1a545 
No aws test on forks
@maxulysse
update GATK and fix Freebayes-Mutect2 channels issue
ca34d7f
@maxulysse
update CHANGELOG
47fa736
@maxulysse
Merge pull request nf-core#214 from MaxUlysse/Mutect2Freebayes
77073c5 
update GATK and fix Freebayes-Mutect2 channels issue
@ggabernet
update aws tests GitHub actions workflows
d58d490
@ggabernet
update changelog
7eff17a
@ggabernet
awstest update env var
245c24e
@ggabernet
awsfulltest fix s3 bucket env var
078b979
@ggabernet
aws test update secrets names
1bcbe18
@ggabernet @maxulysse
Update CHANGELOG.md
4c8d60c 
Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se>
@ggabernet
Merge pull request nf-core#219 from ggabernet/awstest
d43aec9 
update aws tests GitHub actions workflows
@FriederikeHanssen
Replace tmp_dir directory in BaseRecalibration
4422667
@FriederikeHanssen
Merge pull request nf-core#221 from FriederikeHanssen/tmp
c6a4e9d 
Replace tmp_dir directory in BaseRecalibration
@maxulysse
bump version to 2.6.1 (nf-core tools + manual)
51a9923
@maxulysse
update CHANGELOG
2860623
@maxulysse maxulysse added the release This PR is for a release label Jun 22, 2020
@maxulysse maxulysse requested review from ggabernet and a team June 22, 2020 15:02
@apeltzer
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Yeah the PR comes from your branch so the branch checks fail for a reason, shouldn't be bad ;-)

ggabernet
ggabernet reviewed Jun 22, 2020
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@ggabernet ggabernet left a comment •
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I just have two comments in main.nf that I could not add directly as these lines have not been changed.

The rest is not important, we can also adapt it once the AWS has actually full tests

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@ggabernet
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In line 2709 of main.nf :
The indentation is weird.

And in line 2710 of main.nf a channel is created that I think it is not used afterward (or I could not find it).

ewels
ewels reviewed Jun 22, 2020
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@maxulysse
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In line 2709 of main.nf :
The indentation is weird.

And in line 2710 of main.nf a channel is created that I think it is not used afterward (or I could not find it).

Fixed your comments with #223 that was just merged.
And I updated this branch.

So I think we're good to go ;-)

@ggabernet
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ok, great! Is it normal that one of the CI tests (annotation) fails?

@maxulysse
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ok, great! Is it normal that one of the CI tests (annotation) fails?

I don't know why the circleci was not triggered on this PR.
Maybe it's because it's coming from my fork.

But basically the images for the annotation are not built, but they will be built once the PR is merged.

Worst case scenario, I can still build them all myself.

I can actually build the one for the tests now if you like.

ggabernet
ggabernet approved these changes Jun 23, 2020
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LGTM!

@ggabernet
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All good, whatever works best for you :)

@maxulysse maxulysse merged commit bce378e into nf-core:master Jun 23, 2020
@maxulysse maxulysse deleted the 2.6.1 branch July 23, 2020 12:54
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@ggabernet ggabernet ggabernet approved these changes

@apeltzer apeltzer apeltzer approved these changes

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5 participants
@maxulysse @apeltzer @ggabernet @ewels @FriederikeHanssen