package bistro

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package bistro

bistro
- Bistro
  - Command
  - EDSL
  - Path
  - Std
    
    Unix_tools
    
    binary_file
    
    bz2
    
    directory
    
    file
    
    gz
    
    html
    
    marshalled_value
    
    pdf
    
    png
    
    sexp_value
    
    svg
    
    tar
    
    text_file
    
    tsv
    
    zip
  - Template
  - U
  - Workflow
  - directory
bistro.bioinfo
- Bistro_bioinfo
  - Bed
  - Bedtools
    
    Cmd
  - Bowtie
  - Bowtie2
  - ChIPQC
  - Deeptools
    
    compressed_numpy_array
    
    deeptools_matrix
  - Defs
    
    bam
    
    bed3
    
    bed4
    
    bed5
    
    bed6
    
    fasta
    
    fastq
    
    gff
    
    gff2
    
    gff3
    
    sam
    
    sra
  - Deseq2
    
    table
  - Ensembl
  - FastQC
  - Fastq
  - Fastq_screen
  - Htseq
    
    count_tsv
  - Jaspar
  - Macs
    
    narrow_peaks
    
    peak_summits
    
    peaks_xls
  - Macs2
    
    broad_peaks
    
    narrow_peaks
    
    peak_summits
    
    peaks_xls
  - Meme_suite
  - Misc
    
    Infix
  - Prokka
  - Samtools
  - Spades
  - Sra
  - Sra_toolkit
  - Srst2
  - Std
    
    bed3
    
    bed4
    
    bed5
    
    bed6
    
    fasta
    
    fastq
    
    gff
    
    sam
    
    sra
  - Tophat
  - Ucsc_gb
    
    Lift_over
    
    chain_file
    
    bedGraph
    
    bigBed
    
    bigWig
    
    chrom_sizes
    
    twobit
    
    wig
bistro.engine
- Bistro_engine
  - Allocator
  - Db
  - Lwt_utils
  - Scheduler
    
    DAG
    
    logger
    
    logger
  - Task
bistro.tdag
- Bistro_tdag
  - Tdag
    
    Make
    
    D
    
    Allocator
    
    Task
    
    Thread
    
    logger
  - Tdag_sig
    
    Domain
    
    Allocator
    
    Task
    
    Thread
    
    S
    
    logger
bistro.utils
- Bistro_utils
  - Console_logger
  - Dot_output
  - Html_logger
  - Logger
  - Repo
  - Term
    
    Syntax
    
    Let_syntax

Legend:
Library
Module
Module type
Parameter
Class
Class type

Standard definitions

type 'a workflow = 'a Workflow.t

type nonrec ('a, 'b) selector = ('a, 'b) selector

type nonrec docker_image = docker_image

class type 'a directory = object ... end

Conventional type to represent directory targets

class type file = object ... end

Conventional type to represent file targets. The object type is to represent properties of the file, like the type of encoding (text or binary) or the format.

class type binary_file = object ... end

class type 'a marshalled_value = object ... end

Conventional type to represent OCaml values saved with the Marshal module.

class type 'a zip = object ... end

class type 'a gz = object ... end

class type 'a bz2 = object ... end

class type 'a tar = object ... end

class type text_file = object ... end

class type 'a sexp_value = object ... end

Conventional type to represent OCaml values saved as S-expressions.

class type pdf = object ... end

class type html = object ... end

class type png = object ... end

class type svg = object ... end

class type tsv = object ... end

module Unix_tools : sig ... end