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

bowtieMapping

bowtieMapping (From sra download)

flowchart TD
    p0((Channel.fromList))
    p1[bowtieMapping:sra:downloadFiles]
    p2(( ))
    p3(( ))
    p4[bowtieMapping:sra:bowtie]
    p5[bowtieMapping:sra:PCRDuplicates]
    p6(( ))
    p0 -->|ids| p1
    p1 --> p4
    p2 -->|indexfiles| p4
    p3 -->|indexFileBasename| p4
    p4 --> p5
    p5 --> p6

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bowtieMapping (from local files)

flowchart TD
    p0((Channel.fromFilePairs))
    p1(( ))
    p2(( ))
    p3[bowtieMapping:local:bowtie]
    p4[bowtieMapping:local:PCRDuplicates]
    p5(( ))
    p0 -->|files| p3
    p1 -->|indexfiles| p3
    p2 -->|indexFileBasename| p3
    p3 --> p4
    p4 --> p5

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Description of nextflow configuration parameters:

param	value type	description
inputFilePath	string	Path to input file
outputDir	string	Path to where you would like output files stored
databaseFasta	string	Path to the fasta file that you would like to use a the database for Psipred
preconfiguredDatabase	boolean	Are you using a preconfigured database?
writeBedFile	boolean	If you would like to output an additional bedfile.
isSingleEnd	boolean	Is the data single-end or paired-end?
isColorspace	boolean	Is the data colorspace data?
removePCRDuplicates	boolean	Would you like PCR duplicates removed?
input	path	Path to input tsv file if downloading from sra or path to directory holding input files
downloadMethod	string	Either 'sra' or 'local'
databaseFileDir	path	Path to database file dir
indexFileBasename	string	Basename for bt2 files. Ex "index" if files start index.1.bt2, index.2.bt2, etc
mateAQual	path	Path to qual file for mateA
mateBQual	path	Path to qual fiel for mateB

Get Started

• Install Nextflow

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

• Run the script

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