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

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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