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site_name: Biopet User Manual
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pages:
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- Home: 'index.md'
- General:
    - Config: 'general/config.md'
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    - Requirements: 'general/requirements.md'
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    - Memory behaviour: 'general/memory.md'
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    - About: 'general/about.md'
    - License: 'general/license.md'
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- Pipelines:
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    - Basty (Snp typing): 'pipelines/basty.md'
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    - Bam2Wig: 'pipelines/bam2wig.md'
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    - Carp (chip-seq): 'pipelines/carp.md'
    - Flexiprep (QC): 'pipelines/flexiprep.md'
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    - Gears (Metagenome): 'pipelines/gears.md'
    - Gentrap (RNA-seq): 'pipelines/gentrap.md'
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    - Kopisu (CNV Calling): 'pipelines/kopisu.md'
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    - Mapping (Alignment): 'pipelines/mapping.md'
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    - Sage: 'pipelines/sage.md'
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    - Shiva (variantcalling): 'pipelines/shiva.md'
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    - TinyCap (smallRNA): 'pipelines/tinycap.md'
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    - Toucan (Annotation): 'pipelines/toucan.md'
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- Tools:
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    - AnnotateVcfWithBed: 'tools/AnnotateVcfWithBed.md'
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    - BaseCounter: 'tools/BaseCounter.md'
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    - BastyGenerateFasta: 'tools/BastyGenerateFasta.md'
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    - BedToInterval: 'tools/BedToInterval.md'
    - BedtoolsCoverageToCounts: 'tools/BedtoolsCoverageToCounts.md'
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    - BiopetFlagstat: 'tools/BiopetFlagstat.md'
    - CheckAllelesVcfInBam: 'tools/CheckAllelesVcfInBam.md'
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    - DownloadNcbiAssembly: 'tools/DownloadNcbiAssembly.md'
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    - ExtractAlignedFastq: 'tools/ExtractAlignedFastq.md'
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    - FastqFilter: 'tools/FastqFilter.md'
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    - FastqSplitter: 'tools/FastqSplitter.md'
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    - FastqSync: 'tools/FastqSync.md'
    - FindOverlapMatch: 'tools/FindOverlapMatch.md'
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    - FindRepeatsPacBio: 'tools/FindRepeatsPacBio.md'
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    - GvcfToBed: 'tools/GvcfToBed.md'
    - MergeAlleles: 'tools/MergeAlleles.md'
    - MergeTables: 'tools/MergeTables.md'
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    - MpileupToVcf: 'tools/MpileupToVcf.md'
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    - PrefixFastq: 'tools/PrefixFastq.md'
    - SageCountFastq: 'tools/SageCountFastq.md'
    - sagetools: 'tools/sagetools.md'
    - SamplesTsvToConfig: 'tools/SamplesTsvToConfig.md'
    - SeqStat: 'tools/SeqStat.md'
    - SquishBed: 'tools/SquishBed.md'
    - SummaryToTsv: 'tools/SummaryToTsv.md'
    - ValidateFastq: 'tools/ValidateFastq.md'
    - ValidateVcf: 'tools/ValidateVcf.md'
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    - VcfFilter: 'tools/VcfFilter.md'
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    - VcfToTsv: 'tools/VcfToTsv.md'
    - VcfWithVcf: 'tools/VcfWithVcf.md'
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    - VepNormalizer: 'tools/VepNormalizer.md'
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    - WipeReads: 'tools/WipeReads.md'
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- Release notes:
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    - 0.7.0: 'releasenotes/release_notes_0.7.0.md'
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    - 0.6.0: 'releasenotes/release_notes_0.6.0.md'
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    - 0.5.0: 'releasenotes/release_notes_0.5.0.md'
    - 0.4.0: 'releasenotes/release_notes_0.4.0.md'
    - 0.3.2: 'releasenotes/release_notes_0.3.2.md'
    - 0.3.1: 'releasenotes/release_notes_0.3.1.md'
    - 0.3.0: 'releasenotes/release_notes_0.3.0.md'
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- Developer:
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    - Getting Started: 'developer/getting-started.md'
    - Code Style: 'developer/code-style.md'
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    - Example Dependecies: 'developer/example-depends.md'
    - Example Pipeline: 'developer/example-pipeline.md'
    - Example Tool: 'developer/example-tool.md'
    - Example Pipeable: 'developer/example-pipeable.md'
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    - Scala docs: 'developer/scaladocs.md'
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#- ['developing/Setup.md', 'Developing', 'Setting up your local development environment']
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#theme: readthedocs
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repo_url: https://github.com/biopet/biopet