This pipeline takes gzipped fastq files and outputs .bam files aligned to NC_045512.2 as well as consensus fastas. Notably this pipeline incorporates primerclip. By default input files should be paired-end fastq files to cover the 116-255 bp amplicons produced from the Swift Amplicon SARS-CoV-2 Panel. Expected format is *.R1.paired.fastq.gz and *.R2.paired.fastq.gz. --SINGLE_END can also be specified for single end reads.
| Command | Description |
|---|---|
| --INPUT | Input folder where gzipped fastqs are located. For current directory, ./ can be used. |
| --OUTDIR | Output folder where .bams and consensus fastas will be piped into. |
| --SINGLE_END | Flag to indicate input reads are single end. By default this pipeline expects paired end reads. |
| --NO_CLIPPING | Skip primerclip option for shotgun/CovidSeq runs. |
| --SGRNA_COUNT | Add extra step to count sgRNAs. |
| --VARIANTS | Specify which Swift primerset to use. Default: v1. |
| -resume | nextflow will pick up where it left off if the previous command was interrupted for some reason. |
| -with-docker ubuntu:18.04 | Runs command with Ubuntu docker. |
| -with-trace | Outputs a trace.txt that shows which processes end up in which work/ folders. |
Example paired fastqs are provided in the example/ folder. These can be run with the command:
- Example command for example fastqs:
nextflow run greninger-lab/covid_swift_pipeline --INPUT example/ --OUTDIR output/ --PAIRED_END -resume -with-trace with-docker ubuntu:18.04