-
This pipeline is written in Nextflow.
-
If you want to run through Docker, follow the Docker installation guide for Ubuntu.
- Download this github repository using
git clone
.
git clone https://github.com/lanadelrea/Katmon
- Navigate to the directory where
Katmon
is downloaded. Run the pipeline by indicating the path to the input and output folders. The input directory should contain fasta, fastq, bam, and bam index files. Remove the slash "/" after the input and output directory. You can run the pipeline using docker or conda by indicating the-profile
.
nextflow run Katmon --in_dir <input dir> --out_dir <output dir> -profile <docker or conda>
For example:
nextflow run Katmon --in_dir /Samples --out_dir /Results -profile docker
You can also view the help documentations by:
nextflow run Katmon --help
Output directory will have 7 folders containing results from each step used to test for SARS-CoV-2 variant coinfection. The summary report is in the final folder named 07-Report
with the file name as summary-report.html
.