mkdocs.yml

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']
#- ['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