NF_MPXV_F13L

MPXV consensus genome assembly and variants reporting in F13L using ON563414.3 as reference.

Methods

• Trim reads with fastp (default minimum length 100bp)
• Consensus genome assembly using BBMap and iVar consensus
  • minimum coverage of 10
  • minimum base quality of 20
  • minimum frequency threshold of 0.6
• Variants reporting in F13L using iVar variants
  • minimum coverage of 10
  • minimum base quality of 20
  • minimum frequency threshold of 0.01
• Generate summary and QC stats

Usage

Install Nextflow

Install Docker

To run Revica:

nextflow run asereewit/nf_mpxv_f13l -r main -latest --input example_samplesheet.csv --output example_output

with Docker:

nextflow run asereewit/nf_mpxv_f13l -r main -latest --input example_samplesheet.csv --output example_output -profile docker

on AWS:

nextflow run asereewit/nf_mpxv_f13l -r main -latest --input example_samplesheet.csv --output example_output -profile docker -c your_nextflow_aws.config

Options

Option	Explanation
--input	samplesheet in csv format with fastq information
--output	output directory (default: nf_mpxv_f13l_output)
--run_name	name for the summary tsv file (default: 'run')
--skip_fastqc	skip quality control using FastQC (default: false)
--skip_fastp	skip adapters and reads trimming using fastp (default: false)
--min_trim_reads	mininum number of trimmed reads required for downstream processes (default: 0)
--trim_len	minimum read length to keep (default:100)
--save_trimmed_reads	save trimmed fastq (default: false)
--sample	downsample fastq to a certain fraction or number of reads
--min_mapped_reads	minimum number of mapped reads for variants and consensus calling (default: 1000)
--ivar_variants_t	minimum frequency threshold to call consensus (default: 0.01)
--ivar_variants_q	minimum quality score threshold to call consensus (default: 20)
--ivar_variants_m	minimum depth to call consensus (default: 10)
--save_mpileup	save samtools mpileup used for iVar variants
--ivar_consensus_t	minimum frequency threshold to call consensus (default: 0.6)
--ivar_consensus_q	minimum quality score threshold to call consensus (default: 20)
--ivar_consensus_m	minimum depth to call consensus (default: 10)

Usage notes

• Samplesheet example: assets/samplesheet.csv
• You can create a samplesheet using the bundled python script: python bin/fastq_dir_samplesheet.py fastq_dir samplesheet_name.csv
• Memory and CPU usage for pipeline processes can be adjusted in conf/base.config
• Process arguments can be adjusted in conf/modules.config
• If you are using Docker on Linux, check out these post-installation steps (especially cgroup swap limit capabilities support) for configuring Linux to work better with Docker.- By default, Docker has full access to full RAM and CPU resources of the host, but if you are using MacOS, go to Settings -> Resources in Docker Desktop to make sure enough resources are allocated to docker containers.

Contact

For bug reports please email aseree@uw.edu or raise an issue on Github.