This Nextflow version of SNVPhyl is based on the original SNVPhyl pipeline written by Aaron Petkau. For documentation on the pipeline and how it works see the following links.
This version of the software was run with:
Nextflow version 21.04.3 build 5560 created 21-07-2021 15:09 UTC (11:09 EDT)singularity-ce version 3.8.0
Once you have nextflow and singularity installed then get this repo with either:
git clone https://github.com/DHQP/SNVPhyl_Nextflow.git
or
wget https://github.com/DHQP/SNVPhyl_Nextflow/releases/download/1.0.0/SNVPhyl_Nextflow.tar.gz
tar -xvzf SNVPhyl_Nextflow.tar.gz
To run the pipeline do the following:
nextflow run snvphyl.nf --outdir ./results -c snvphyl.config --refgenome reference.fasta
Make sure to pick an appropriate reference fasta file for your samples! The one included in this repository is just for example purposes.
==============================================================================================================================
I N P U T P A R A M E T E R S
==============================================================================================================================
--refgenome Reference Genome [Default "reference.fasta"] : reference.fasta
--input_reads Input folder with reads [Default "./FASTQs/"] : ./FASTQs/
--outdir Output Directory [Default "./results"] : ./test
--window_size Window size for identifying high-density SNV regions [Default "11"] : 11
--density_threshold SNV threshold for identifying high-density SNV regions [Default "2"] : 2
The config file is currently run locally with containers using Singularity. Alternatively you can adjust the config file to run with a different executors or Docker.
Prior to running you will need to change the singularity.cacheDir = '$PATH/Singularity_Containers' in line 25 of the config file to the location of your singularity cache directory.
The following files will be output by SNVPhyl and are explained in the original SNVPhyl Documentation.
- filterStats.txt
- phylogeneticTree.newick
- phylogeneticTreeStats.txt
- snvAlignment.phy
- snvTable.tsv
- snvMatrix.tsv
- vcf2core.tsv
Additionally, two other files are created by this workflow.
- Log_File.txt -- Contains information on the software versions used for this run.
- report.html -- This is the nextflow report that will tell you the CPU usage, time to run each job and RAM requirements.
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