package bistro

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package bistro

bistro
- Bistro
  - Private
  - Shell_dsl
  - Template_dsl
  - Workflow
  - binary_file
  - bz2
  - directory
  - file
  - gz
  - html
  - pdf
  - png
  - sexp_value
  - svg
  - tar
  - text_file
  - tsv
  - zip
bistro.bioinfo
- Bistro_bioinfo
  - Bed
  - Bedtools
    
    Cmd
  - Bowtie
    
    index
  - Bowtie2
    
    index
  - ChIPQC
    
    output
  - Cisa
  - DESeq2
    
    table
  - Deeptools
    
    compressed_numpy_array
    
    deeptools_matrix
  - Ensembl
  - FastQC
    
    report
  - Fastq
  - Fastq_screen
    
    output
  - Hisat2
  - Htseq
    
    count_tsv
  - Idba
  - Idr
  - Kallisto
    
    abundance_table
    
    index
  - Macs
    
    narrow_peaks
    
    output
    
    peak_summits
    
    peaks_xls
  - Macs2
    
    broad_output
    
    broad_peaks
    
    narrow_output
    
    narrow_peaks
    
    output
    
    peak_summits
    
    peaks_xls
  - Meme_suite
  - Picardtools
  - Prokka
  - Quast
  - Samtools
  - Spades
  - Sra_toolkit
  - Srst2
  - Star
  - Subread
    
    count_table
  - Tophat
    
    output
  - Ucsc_gb
    
    Lift_over
    
    chain_file
    
    output
    
    bedGraph
    
    bigBed
    
    bigWig
    
    chrom_sizes
    
    chromosome_sequences
    
    twobit
    
    wig
  - bam
  - bed3
  - bed4
  - bed5
  - bed6
  - fasta
  - fastq
  - gff
  - gff2
  - gff3
  - indexed_bam
  - phred64_fastq
  - sam
  - sanger_fastq
  - solexa_fastq
  - sra
bistro.engine
- Bistro_engine
  - Allocator
  - Db
  - Docker
  - Eval_thread
    
    Infix
  - Execution_env
  - Execution_trace
    
    Set
  - Local_backend
  - Logger
    
    t
  - Lwt_queue
  - Misc
  - Path
  - Scheduler
    
    Backend
    
    Gc
    
    Make
    
    Backend
  - Shell_command
  - Singularity
  - Task_result
bistro.internals
- Bistro_internals
  - Command
    
    Docker_image
    
    Singularity_image
  - Template
  - Workflow
    
    Any
    
    Map
    
    Set
    
    Table
bistro.multinode
- Bistro_multinode
  - Client
  - Server
bistro.nlp
- Bistro_nlp
  - Stanford_parser
    
    deps
bistro.unix
- Bistro_unix
  - Cmd
bistro.utils
- Bistro_utils

Legend:
Library
Module
Module type
Parameter
Class
Class type

type 'a sample = {

id : string;
tissue : string;
factor : string;
replicate : string;
bam : indexed_bam Bistro.pworkflow;
peaks : bed3 as 'a Bistro.pworkflow;

}

class type output = object ... end

val run : 'a sample list -> output Bistro.pworkflow

Beware: doesn't work with only one sample (see https://support.bioconductor.org/p/84754/)