Code

Add some Variant Calling#4

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maxulysse merged 39 commits intonf-core:devnf-core/sarek:devfrom maxulysse:nf-core_VCmaxulysse/nf-core_sarek:nf-core_VCCopy head branch name to clipboardMay 3, 2019

+489-46

Commits

Commits on May 1, 2019

• update README

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  7b1833d

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• update .travis.yml

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  961856c

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• add Jenkinsfile

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• update conda environment file

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

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Commits on May 2, 2019

• update software_version collect

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• trying to fix travis CI

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• only one env

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• remove pip upgrade

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• remove lint

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• remove lib/SarekUtils.groovy

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• add References to .gitignore

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• lower case

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• remove picard

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• improve software versions gathering

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• fix docker owner

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• update tests

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• sort params

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• add preprocessing

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• improve TSV localisation

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• improve multiple TSV

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• add parrallelized BaseRecalibrator

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• smaller test on travisCI

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• try to fix path to data

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• include building reference when testing...

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• reorganize tests

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• reduce memory and cpus

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• add tests

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• add flowcellLaneFromFastq function

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• Merge remote-tracking branch 'upstream/dev' into nf-core

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• update allelecount to 4.0.2

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• add HaplotypeCaller

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Commits on May 3, 2019

• improve Jenkins tests

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• update GATK to 4.1.2.0

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• update docs

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• add single Strelka and single Manta

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• add tests

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• specify -ansi-log false for testing

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• specify -ansi-log false for testing

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