mkdocs.yml 2.12 KB
Newer Older
1
site_name: Biopet User Manual
2
pages:
3 4 5
- Home: 'index.md'
- General:
    - Config: 'general/config.md'
6
    - Requirements: 'general/requirements.md'
Peter van 't Hof's avatar
Peter van 't Hof committed
7 8
    - About: 'general/about.md'
    - License: 'general/license.md'
9
- Pipelines:
10
    - Basty (Snp typing): 'pipelines/basty.md'
Peter van 't Hof's avatar
Peter van 't Hof committed
11
    - Bam2Wig: 'pipelines/bam2wig.md'
12 13
    - Carp (chip-seq): 'pipelines/carp.md'
    - Flexiprep (QC): 'pipelines/flexiprep.md'
Wai Yi Leung's avatar
Wai Yi Leung committed
14 15
    - Gears (Metagenome): 'pipelines/gears.md'
    - Gentrap (RNA-seq): 'pipelines/gentrap.md'
16
    - Mapping (Alignment): 'pipelines/mapping.md'
17
    - Sage: 'pipelines/sage.md'
Wai Yi Leung's avatar
Wai Yi Leung committed
18 19
    - Shiva (variantcalling): 'pipelines/shiva.md'
    - Toucan (Annotation): 'pipelines/toucan.md'
20 21
- Tools:
    - SamplesTsvToJson: 'tools/SamplesTsvToJson.md'
Wai Yi Leung's avatar
Wai Yi Leung committed
22 23
    - BedToInterval: 'tools/bedtointerval.md'
    - BastyGenerateFasta: 'tools/BastyGenerateFasta.md'
24 25 26 27 28 29 30 31 32 33
    - 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'
    - MpileupToVcf: 'tools/MpileupToVcf.md'
    - Sagetools: 'tools/sagetools.md'
    - WipeReads: 'tools/WipeReads.md'
Wai Yi Leung's avatar
Wai Yi Leung committed
34 35
    - VcfFilter: 'tools/VcfFilter.md'
    - VepNormalizer: 'tools/VepNormalizer.md'
36
- Release notes:
Wai Yi Leung's avatar
Wai Yi Leung committed
37
    - 0.5.0: 'release_notes_0.5.0.md'
38 39 40 41
    - 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'
Peter van 't Hof's avatar
Peter van 't Hof committed
42
- Developer:
Peter van 't Hof's avatar
Peter van 't Hof committed
43 44
    - Getting Started: 'developer/getting-started.md'
    - Code Style: 'developer/code-style.md'
45 46 47 48
    - Example pipeline: 'developer/example-pipeline.md'
    - Example tool: 'developer/example-tool.md'
    - Example reporting: 'developer/example-reporting.md'
    - Example pipeable: 'developer/example-pipeable.md'
Peter van 't Hof's avatar
Peter van 't Hof committed
49 50
    - Scala docs:
      - 0.4.0: 'developer/code-style.md'
51
#- ['developing/Setup.md', 'Developing', 'Setting up your local development environment']
52
#theme: readthedocs
Peter van 't Hof's avatar
Peter van 't Hof committed
53
repo_url: https://github.com/biopet/biopet