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Final polishing#164

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maxulysse merged 24 commits intonf-core:devnf-core/sarek:devfrom maxulysse:Mutect2maxulysse/nf-core_sarek:Mutect2Copy head branch name to clipboardMar 27, 2020

+183-124

Commits

Commits on Mar 18, 2020

• small refactor

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Commits on Mar 19, 2020

• check for all references

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Commits on Mar 20, 2020

• Merge remote-tracking branch 'upstream/dev' into Mutect2

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• update docs

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• indentation

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• sort contributors

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  6ed31e4

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• more comments

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• fix links to GTA CI

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Commits on Mar 23, 2020

• add vcf concatenated to annotation

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Commits on Mar 25, 2020

• typo

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Commits on Mar 26, 2020

• typo

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• update gatkspark from 4.1.4.1 to 4.1.6.0

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• test changing URLs

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• update URLs

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Commits on Mar 27, 2020

• add --no_gatk_spark params

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• add tests for GATKspark

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  b9d41c2

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• fix typo

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• fix paths to files

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• typo in params name

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• fix MarkDuplicates output with --no_gatk_spark params

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  0fe3e23

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• fix comments

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• improve CHANGELOG

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• update rules for markdownlint

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  828a4b7

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• Apply suggestions from code review

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