nextflowViral

This set of pipelines represents a viral genomic SNPs and consensus computing utility with a minimum number of software dependencies compared to comparable tools. The nextflowViral pipelines also leverage Singularity for enhanced portability.

Vignette 1: Install and run from LINUX/UNIX using Singularity and Nextflow only - Recommended Method

Vignette 1a: When singularity is already installed and nextflow can be installed from the local HPC Cluster

tar xvfz bowtieConsensTestFiles.tar.gz

module load nextflow/24.04.2

nextflow run prepReferenceOnly.singularity.nf --makeReference "$PWD/bowtieConsensTestFiles/eng_live_atten_poliovirus/MZ245455.1.fasta" --indexDir "$PWD/bowtieConsensTestFiles/eng_live_atten_poliovirus/"

Running main pipeline with default inputs from $PWD/bowtieConsensTestFiles/eng_live_atten_poliovirus/

nextflow run consensHiCovFromPairedFastq.singularity.nf

After successful run, folder output/ should contain polio-sample-8_S13_R.bedGraph, *.bedGraph.FiveX, *.fasta, *.fiveX.fasta, *.snp.tsv, *.vcf, *.vcf.gz, and *.vcf.gz.csi. The file, polio-sample-8_S13_R.snp.tsv, should contain 1 SNP position.

Additional use cases for consensHiCovFromPairedFastq.singularity.nf coming soon

Vignette 1b: Installation of singularity, nexflow, or both through Miniconda - Coming Soon

Vignette 2: Install prereqs for running local HPC Cluster consensusFromPairedFastq.nf

module load nextflow/24.04.2

module load bowtie2/2.3.5.1

module load samtools/1.9

module load bcftools/1.9

module load htslib/1.19.1

module load bedtools/2.27.1

module load seqtk/1.3

Vignette 2a: Set '--local true' flag, otherwise, no command line arguments for input/output.

nextflow run consensHiCovFromPairedFastq.singularity.nf --local

After successful run, folder output/ should contain polio-sample-8_S13_R.bedGraph, *.bedGraph.FiveX, *.fasta, *.fiveX.fasta, *.snp.tsv, *.vcf, *.vcf.gz, and *.vcf.gz.csi. The file, polio-sample-8_S13_R.snp.tsv, should contain 1 SNP position.

Vignette 2b: Set '--local true' flag and provide --reference and --inputPair as input arguments.

nextflow run consensHiCovFromPairedFastq.singularity.nf --local --reference "$PWD/bowtieConsensTestFiles/EnterovirusD70/MT081369_JPN_1989-23292" --inputPair "$PWD/bowtieConsensTestFiles/EnterovirusD70/EnterovirusD70_SRR13402413_R{1,2}_001.fastq.gz"

After successful run, folder output/ should contain EnterovirusD70_SRR13402413_R.bedGraph, *.bedGraph.FiveX, *.fasta, *.fiveX.fasta, *.snp.tsv, *.vcf, *.vcf.gz, and *.vcf.gz.csi. The file, EnterovirusD70_SRR13402413_R.snp.tsv, should not contain SNP positions.

To point parameters to other files, be prepared to update parameters, inputPair and reference, in nextflow.config.