Commit 5bed902a authored by Peter van 't Hof's avatar Peter van 't Hof

Upgrade to new version of mkdocs config

parent 38ec7a1d
site_name: Biopet User Manual
pages:
- ['index.md', 'Home']
- ['general/config.md', 'General', 'Config']
- ['pipelines/basty.md', 'Pipelines', 'Basty']
- ['pipelines/bam2wig.md', 'Pipelines', 'Bam2Wig']
- ['pipelines/carp.md', 'Pipelines', 'Carp']
- ['pipelines/gentrap.md', 'Pipelines', 'Gentrap']
- ['pipelines/shiva.md', 'Pipelines', 'Shiva']
- ['pipelines/flexiprep.md', 'Pipelines', 'Flexiprep']
- ['pipelines/mapping.md', 'Pipelines', 'Mapping']
- ['pipelines/sage.md', 'Pipelines', 'Sage']
- ['pipelines/toucan.md', 'Pipelines', 'Toucan']
- ['tools/SamplesTsvToJson.md','Tools','SamplesTsvToJson']
- ['tools/BastyGenerateFasta.md','Tools','BastyGenerateFasta']
- ['tools/bedtointerval.md','Tools','BedToInterval']
- ['tools/bedtoolscoveragetocounts.md','Tools','BedtoolsCoverageToCounts']
- ['tools/BiopetFlagstat.md','Tools','BiopetFlagstat']
- ['tools/CheckAllelesVcfInBam.md','Tools','CheckAllelesVcfInBam']
- ['tools/ExtractAlignedFastq.md','Tools','ExtractAlignedFastq']
- ['tools/FastqSplitter.md', 'Tools','FastqSplitter']
- ['tools/FindRepeatsPacBio.md','Tools','FindRepeatsPacBio']
- ['tools/VcfFilter.md','Tools','VcfFilter']
- ['tools/MpileupToVcf.md', 'Tools', 'MpileupToVcf']
- ['tools/sagetools.md', 'Tools', 'Sagetools']
- ['tools/VepNormalizer.md', 'Tools', 'VepNormalizer']
- ['tools/WipeReads.md', 'Tools', 'WipeReads']
- Home: 'index.md'
- General:
- Config: 'general/config.md'
- Pipelines:
- Basty: 'pipelines/basty.md'
- Bam2Wig: 'pipelines/bam2Wig.md'
- Carp: 'pipelines/carp.md'
- Gentrap: 'pipelines/gentrap.md'
- Shiva: 'pipelines/shiva.md'
- Flexiprep: 'pipelines/flexiprep.md'
- Mapping: 'pipelines/mapping.md'
- Toucan: 'pipelines/toucan.md'
- Sage: 'pipelines/sage.md'
- Tools:
- SamplesTsvToJson: 'tools/SamplesTsvToJson.md'
- BastyGenerateFasta: 'tools/bedtointerval.md'
- BedToInterval: 'tools/bedtointerval.md'
- BedtoolsCoverageToCounts: 'tools/bedtoolscoveragetocounts.md'
- BiopetFlagstat: 'tools/BiopetFlagstat.md'
- CheckAllelesVcfInBam: 'tools/CheckAllelesVcfInBam.md'
- ExtractAlignedFastq: 'tools/ExtractAlignedFastq.md'
- FastqSplitter: 'tools/FastqSplitter.md'
- FindRepeatsPacBio: 'tools/FindRepeatsPacBio.md'
- VcfFilter: 'tools/VcfFilter.md'
- MpileupToVcf: 'tools/MpileupToVcf.md'
- Sagetools: 'tools/sagetools.md'
- VepNormalizer: 'tools/VepNormalizer.md'
- WipeReads: 'tools/WipeReads.md'
- BastyGenerateFasta: 'tools/BastyGenerateFasta.md'
- Release notes:
- 0.4.0: 'release_notes_0.4.0.md'
- 0.3.2: 'release_notes_0.3.2.md'
- 0.3.1: 'release_notes_0.3.1.md'
- 0.3.0: 'release_notes_0.3.0.md'
- About: 'about.md'
- License: 'license.md'
#- ['developing/Setup.md', 'Developing', 'Setting up your local development environment']
- ['release_notes_0.4.0.md', 'Release notes', '0.4.0']
- ['release_notes_0.3.2.md', 'Release notes', '0.3.2']
- ['release_notes_0.3.1.md', 'Release notes', '0.3.1']
- ['release_notes_0.3.0.md', 'Release notes', '0.3.0']
- ['about.md', 'About']
- ['license.md', 'License']
#theme: readthedocs
repo_url: https://git.lumc.nl/biopet/biopet
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