Code

Add minimal genomes possibilities#60

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maxulysse merged 27 commits intonf-core:devnf-core/sarek:devfrom maxulysse:minimalmaxulysse/nf-core_sarek:minimalCopy head branch name to clipboardDec 6, 2019

+518-106

Commits

Commits on Oct 21, 2019

• add minimal genome and update some processes

  maxulysse

  committed
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Commits on Oct 28, 2019

• add smallerGRCh37 and minimalGRCh37

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• use bwa aln when no knowIndels, otherwise use bwa mem, noIntervals currently in the process of being added everywhere

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Commits on Oct 29, 2019

• don't use bwa aln

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• add automatic generation of intervals file based on fastaFai file

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Commits on Nov 4, 2019

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

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

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• add minimal tests

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• fix processes with no intervals

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• add comments

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

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• params noIntervals -> no_intervals

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• sort genomes + add news

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• code polishing

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• update CHANGELOG

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Commits on Dec 2, 2019

• Merge branch 'dev' into minimal

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Commits on Dec 6, 2019

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

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• add --skipQC all and --tools Manta,mpileup,Strelka to minimal genome tests

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• update Nextflow version

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• update Nextflow version

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• update Nextflow

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• add --step annotation to profile

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• don't need to specify step here

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• move params initalization

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• add docs

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• fix markdownlint

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• more complete docs + sort genomes

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