Aims:
Implement an end-to-end bioinformatics workflow that is reproducible, robust, scalable and compute infrastructure agnostic
Leverage from the host plant antiviral response pathway to increase sensitivity and specificity of pathogen detections
Prevent or minimise the reporting of cross-sample contaminations owing to index hopping events (false positive detections)
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We will use two nextflow pipelines to process the Virome data, initially, we run trimgalore to filter out poor quality reads/bases and remove adapter sequences. Then we run VirReport to assess the presence of viruses and viroids.
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2. Run VirReport using a PBS Pro script
Define nextflow configurations if different from provided template:
| Code Block |
|---|
includeConfig 'conf/base.config'
params {
outdir = 'results'
indexfile = 'index.csv'
blast_db_dir = '/lustre/work-lustre/hia_mt18005/blastDB/30112021'
blast_local_db_path = '/work/img/databases/PVirDB/PVirDB_ver20211109.fasta'
targets = false
targets_file = 'Targetted_Viruses_Viroids.txt'
help = false
cap3_len = '20'
orf_minsize = '150'
orf_circ_minsize = '150'
blastn_evalue = '0.0001'
blastp_evalue = '0.0001'
blastn_method = 'megablast'
blastp = false
spades = false
spadeskmer = '9 11 13 15 17 19 21'
blastlocaldb = false
ictvinfo = 'ICTV_taxonomy_MinIdentity_Species.tsv'
contamination_detection = false
contamination_flag = '0.01'
contamination_detection_method = 'FPKM'
}
process.container = "ghcr.io/eresearchqut/virreport:v1.0.0"
manifest {
name = "eresearchqut/VirReport"
author = "Roberto Barrero, Maely Gauthier, Desmond Schmidt, Craig Windell"
defaultBranch = "main"
description = "VirReport is designed to help phytosanitary diagnostics of viruses and viroid pathogens in quarantine facilities. It takes small RNA-Seq samples as input."
version = "v1.0.0"
} |
Prepare a PBS Pro submission script:
| Code Block |
|---|
#!/bin/bash -l
#PBS -N nftrimgalore
#PBS -l walltime=24:00:00
#PBS -l select=1:ncpus=1:mem=5gb
cd $PBS_O_WORKDIR
NXF_OPTS='-Xms1g -Xmx4g'
module load java
#run netflow pipeline
nextflow run eresearchqut/VirReport -profile singularity --indexfile index.csv |