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Change --sample by --input#23

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maxulysse merged 36 commits intonf-core:devnf-core/sarek:devfrom maxulysse:nf-core-inputmaxulysse/nf-core_sarek:nf-core-inputCopy head branch name to clipboardSep 10, 2019

+312-166

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Commits on Aug 13, 2019

• feat: remove unnecessary Channel.create()

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Commits on Aug 14, 2019

• feat: replace --sample with --input, genomeFile with fasta...

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Commits on Aug 16, 2019

• feat: update comments

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• feat: Add TIDDIT version in MultiQC report

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Commits on Aug 19, 2019

• feat: polish code

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Commits on Aug 27, 2019

• feat: update docs

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Commits on Aug 28, 2019

• Merge branch 'dev' into nf-core-input

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Commits on Sep 2, 2019

• rename genomeFile, genomeIndex and genomeDict in main.nf script

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

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• add deprecation message

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• better deprecation message

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• update docs

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• update docs

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• Merge branch 'nf-core-input' of github.com:MaxUlysse/Sarek into nf-core-input

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Commits on Sep 3, 2019

• Refactor deprecation for --sample, --sampleDir, --anotateVCF, --noReports, --genomeDict, --genomeFile, --genomeIndex

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• move modifications to another branch

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• Fix --input for germline sample directory

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• Add GitHubActions (nf-core#27)

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• fix syntax hopefully

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

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• undo changes

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• set tsvPAth to null at the right place...

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Commits on Sep 4, 2019

• update CHANGELOG

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

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Commits on Sep 5, 2019

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

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  0f3254d

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• better deprecation message

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  580d5f6

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Commits on Sep 6, 2019

• update docs

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  1af9c37

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

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

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  e39f816

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• fix typo in params.fastaFai

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• fix typo in channel pairBamMutect2

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Commits on Sep 9, 2019

• code polishing

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

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• MD linting

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• add deprecation info in docs about --noReports

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Commits on Sep 10, 2019

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

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  committed
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