Skip to content

Latest commit

 

History

History
72 lines (55 loc) · 2.99 KB

README.md

File metadata and controls

72 lines (55 loc) · 2.99 KB
Raw

Nextflow Conversion of ASVTableTask.pm

MarkerGeneAnalysis16sDADA2

flowchart TD
    p0((Channel.fromList))
    p1[markerGeneAnalysis:downloadFiles]
    p2[markerGeneAnalysis:filterFastqs]
    p3[markerGeneAnalysis:buildErrors]
    p4[markerGeneAnalysis:fastqToAsv]
    p5[markerGeneAnalysis:mergeAsvsAndAssignToOtus]
    p6(( ))
    p7(( ))
    p8(( ))
    p0 -->|ids| p1
    p1 --> p2
    p2 --> p3
    p3 --> p4
    p4 --> p5
    p5 --> p8
    p5 --> p7
    p5 --> p6
Loading

Decription of nextflow configuration parameters:

param value type description
studyIdFile path Path to SRAID tsv file
platform string Platform the sequencing was done on. Used in filterFastqs step. Ex: "illumina"
isPaired boolean Is the data paired?
trimLeft int Amount to trim from left. Used in filterFastqs step.
trimLeftR int Amount to trim from reverse strand. Used in filterFastqs step.
truncLen int Amount to truncate from forward strand. Used in filterFastqs step.
truncLenR int Amount to truncate from reverse stand. Used in filterFastqs step.
maxLen int Maximum length. Used in filterFastqs step.
mergeTechReps boolean Would you like to merge TechReps in fastqToAsv step.
trainingSet path Path to training set fasta.
speciesAssignment path Path to species assignment fasta.
outputDir path Path where you would like results to be stored
nValue scientific notation Ex: 1e+02 Used in buildErrors Step. Setting value above 1e+02 can cause issues with memory

In order to run the script, you will need to supply to the nextflow.config file:

  1. An apikey to be used to collect the fastq files from NCBI
  2. The location of your training set file (a short example file has been supplied in /data)
  3. The location of your species assignment file (a short example file has been supplied in /data)

The parameter names for these have already been specified, you only need to enter them into the empty quotes.

The output files from this tool will be formatted as (SRRID supplied in sraStudyIDFile parameter)_(outputName parameter).(nothing, "bootstraps", or "full")

Get Started

  • Install Nextflow

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

  • Run the script

    nextflow run VEuPathDB/MarkerGeneAnalysis16sDADA2 -with-trace -c <config_file> -r main

Running this locally can commonly result in an OOME. This results from the derepFastq function in buildErrorsN.R having n as too great a value.

drpsF[[i]] <- derepFastq(inputFilesF[[i]], n = 1e+06, verbose = verbose)

The default n is 1 million reads. If an OOME occurs, a lower number can be entered.

Ex: drpsF[[i]] <- derepFastq(inputFilesF[[i]],n = 1e+03, verbose = verbose)

This is specified in the nextflow.config file parameter "nValue".

Documentation for derepFastq and other dada2 functionality can be found here.