Skip to content

README.md

Latest commit

 

History

History
42 lines (35 loc) · 1.36 KB

README.md

File metadata and controls

42 lines (35 loc) · 1.36 KB

THIS REPO IS 🚧 UNDER CONSTRUCTION 🚧 and NOT Used in ANY production CODE

Nextflow Conversion of GenomeAlignWithGfClientTask

blat

flowchart TD
    p0((Channel.fromPath))
    p1([splitFasta])
    p2(( ))
    p3[blat:runBlat]
    p4([collectFile])
    p5(( ))
    p0 --> p1
    p1 -->|seqs| p3
    p2 -->|data.2bit| p3
    p3 --> p4
    p4 --> p5
Loading

Get Started

  • Install Nextflow

    curl https://get.nextflow.io | bash

Usage

Main parameters:

param value type description
seqFile string Path to input fasta file
fastaSubsetSize integer How many sequences per split of input file
databasePath string Path to database Files
outputDir string publish directory
maxIntron integer Maximum intron size (Default 750000)
dbType string "dna" / "prot" / "dnax" (DNA sequence translated in six frames to protein). Default is dna.
queryType string "dna" / "prot" / "dnax" (DNA sequence translated in six frames to protein) "rnax" (DNA sequence translated in three frames to protein)
blatParams string Additional parameters for gfClient
trans boolean Translate database to protein in 6 frames

Example

nextflow run https://github.com/VEuPathDB/blat -with-trace -c <config_file> -r main