mkdocs.yml 1.44 KB
Newer Older
1
site_name: Biopet User Manual
2 3
pages:
- ['index.md', 'Home']
4
- ['general/config.md', 'General', 'Config']
5
- ['pipelines/basty.md', 'Pipelines', 'Basty']
bow's avatar
bow committed
6
- ['pipelines/gentrap.md', 'Pipelines', 'Gentrap']
7 8 9 10
- ['pipelines/GATK-pipeline.md', 'Pipelines', 'GATK-pipeline']
- ['pipelines/flexiprep.md', 'Pipelines', 'Flexiprep']
- ['pipelines/mapping.md', 'Pipelines', 'Mapping']
- ['pipelines/sage.md', 'Pipelines', 'Sage']
Sander Bollen's avatar
Sander Bollen committed
11
- ['pipelines/toucan.md', 'Pipelines', 'Toucan']
12 13 14 15 16 17 18 19 20 21 22 23
- ['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']
24
- ['tools/VepNormalizer.md', 'Tools', 'VepNormalizer']
25
- ['tools/WipeReads.md', 'Tools', 'WipeReads']
26
#- ['developing/Setup.md', 'Developing', 'Setting up your local development environment']
27 28
- ['about.md', 'About']
- ['license.md', 'License']
29
#theme: readthedocs
Sander Bollen's avatar
Sander Bollen committed
30
repo_url: https://git.lumc.nl/biopet/biopet