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

Nextflow Conversion of tRNAScanTask.pm

tRNAScan

flowchart TD
    p0((Channel.fromPath))
    p1([splitFasta])
    p2[tRNAScan:runtRNAScan]
    p3([collectFile])
    p4[tRNAScan:fixHeader]
    p5(( ))
    p0 --> p1
    p1 -->|seqs| p2
    p2 --> p3
    p3 --> p4
    p4 --> p5

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Decription of nextflow configuration parameters:

param	value type	description
inputFilePath	string	Path to the input fasta file.
outputDir	string	Path to where you would like output files to be stored.
outputFileName	string	How you would like this output file to be stored.
fastaSubsetSize	integer	How many sequences you would like to have sent to each process at a time.

Get Started

• Install Nextflow

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

• Run the script

  nextflow run VEuPathDB/tRNAScan -with-trace -c <config_file> -r main