Nextflow pipeline for de novo assembly of enterovirus genomes
nextflow run enterovirus.nf --inputfq 'reads/*_R{1,2}_001.fastq.gz' -profile ( slurm | local )
REQUIRED
--inputfq [Fileglob that matches your input reads, must be surrounded with
'single-quotes' prevent shell expansion]
-profile [If you are running this on a SLURM cluster, set to 'slurm' to submit jobs to
the scheduler. If not, set 'local']
OPTIONAL
--output [Path to output directory, 'enterovirus-NF.out' by default]
--bbnorm_target [Kmer normalization target for bbnorm, 5000 by default]
| Filename | File content |
|---|---|
| vapor/{SAMPLENAME}.ref.out | VAPOR statistics |
| vapor/{SAMPLENAME}.ref.fa | VAPOR selected reference sequence |
| mapping/{SAMPLENAME}.assembly_mapping.sorted.bam | Reads mapped to sample assembly |
| mapping/{SAMPLENAME}.reference_mapping.sorted.bam | Reads mapped to reference sequence |
| mapping/{SAMPLENAME}.assembly_mapping.normalized.sorted.bam | Normalized reads mapped to assembly |
| assembly/{SAMPLENAME}.iva.fa | Sample assembly |
| assembly/{SAMPLENAME}.shiver.fa | Sample assembly post-processed with Shiver |
- Nextflow (https://www.nextflow.io/)
- Conda (Install miniconda: https://docs.conda.io/en/latest/miniconda.html)
- Conda channels bioconda and conda-forge (https://bioconda.github.io/#set-up-channels)