package bistro

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bistro
- Library bistro
  - Bistro
    
    file
    
    directory
    
    Template_dsl
    
    Shell_dsl
    
    Workflow
    
    Private
    
    text_file
    
    sexp_value
    
    binary_file
    
    pdf
    
    html
    
    png
    
    svg
    
    tsv
    
    zip
    
    gz
    
    bz2
    
    tar
- Library bistro.bioinfo
  - Bistro_bioinfo
    
    bam
    
    bed3
    
    bed4
    
    bed5
    
    bed6
    
    fasta
    
    fastq
    
    sanger_fastq
    
    solexa_fastq
    
    phred64_fastq
    
    gff
    
    gff2
    
    gff3
    
    indexed_bam
    
    sam
    
    sra
    
    Bed
    
    Fastq
    
    Ucsc_gb
    
    twobit
    
    chrom_sizes
    
    bigBed
    
    bedGraph
    
    wig
    
    bigWig
    
    chromosome_sequences
    
    Lift_over
    
    chain_file
    
    output
    
    Ensembl
    
    Bedtools
    
    Cmd
    
    Deeptools
    
    compressed_numpy_array
    
    deeptools_matrix
    
    Htseq
    
    count_tsv
    
    Samtools
    
    Picardtools
    
    Sra_toolkit
    
    Subread
    
    count_table
    
    ChIPQC
    
    output
    
    FastQC
    
    report
    
    Fastq_screen
    
    output
    
    Bowtie
    
    index
    
    Bowtie2
    
    index
    
    Tophat
    
    output
    
    Hisat2
    
    Star
    
    Kallisto
    
    index
    
    abundance_table
    
    Spades
    
    Idba
    
    Cisa
    
    Quast
    
    DESeq2
    
    table
    
    Macs
    
    output
    
    peaks_xls
    
    narrow_peaks
    
    peak_summits
    
    Macs2
    
    output
    
    narrow_output
    
    broad_output
    
    peaks_xls
    
    narrow_peaks
    
    peak_summits
    
    broad_peaks
    
    Idr
    
    Meme_suite
    
    Prokka
    
    Srst2
- Library bistro.engine
  - Bistro_engine
    
    Allocator
    
    Db
    
    Docker
    
    Eval_thread
    
    Infix
    
    Execution_env
    
    Execution_trace
    
    Set
    
    Local_backend
    
    Logger
    
    t
    
    Lwt_queue
    
    Misc
    
    Path
    
    Scheduler
    
    Gc
    
    Backend
    
    Make
    
    Shell_command
    
    Singularity
    
    Task_result
- Library bistro.internals
  - Bistro_internals
    
    Command
    
    Docker_image
    
    Singularity_image
    
    Template
    
    Workflow
    
    Any
    
    Set
    
    Table
    
    Map
- Library bistro.multinode
  - Bistro_multinode
    
    Client
    
    Server
- Library bistro.nlp
  - Bistro_nlp
    
    Stanford_parser
    
    deps
- Library bistro.unix
  - Bistro_unix
    
    Cmd
- Library bistro.utils
  - Bistro_utils
    
    Console_logger
    
    Dot_output
    
    Html_logger
    
    Html_report
    
    R_script
    
    Repo
- Library ppx_bistro
  - Ppx_bistro
    
    L
    
    B
    
    Located
    
    payload_rewriter
    
    ast_translation
- Sources
  - bistro
    
    bistro.ml
  - bistro.bioinfo
    
    bistro_bioinfo.ml
  - bistro.engine
    
    allocator.ml
    
    bistro_engine.ml
    
    db.ml
    
    docker.ml
    
    eval_thread.ml
    
    execution_env.ml
    
    execution_trace.ml
    
    local_backend.ml
    
    logger.ml
    
    lwt_queue.ml
    
    misc.ml
    
    path.ml
    
    scheduler.ml
    
    shell_command.ml
    
    singularity.ml
    
    task_result.ml
  - bistro.internals
    
    bistro_internals.ml
    
    command.ml
    
    template.ml
    
    workflow.ml
  - bistro.multinode
    
    bistro_multinode.ml
  - bistro.nlp
    
    bistro_nlp.ml
  - bistro.unix
    
    bistro_unix.ml
  - bistro.utils
    
    bistro_utils.ml
    
    console_logger.ml
    
    dot_output.ml
    
    html_logger.ml
    
    html_report.ml
    
    r_script.ml
    
    repo.ml
  - ppx_bistro
    
    ppx_bistro.ml
    
    ppx_bistro__.ml
    
    script_parser.ml

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Module `Bistro_bioinfo.Picardtools`

val img : Bistro.Shell_dsl.container_image list

val markduplicates : 
  ?remove_duplicates:bool ->
  [ `indexed_bam ] Bistro.dworkflow ->
  [ `picard_markduplicates ] Bistro.dworkflow

val reads : [ `picard_markduplicates ] Bistro.dworkflow -> bam Bistro.pworkflow

val sort_bam_by_name : bam Bistro.pworkflow -> bam Bistro.pworkflow

package bistro

Module Bistro_bioinfo.Picardtools

Module `Bistro_bioinfo.Picardtools`