https://github.com/dfornika/pangolin-simple
Simple nextflow pipeline for running pangolin
https://github.com/dfornika/pangolin-simple
Last synced: 3 months ago
JSON representation
Simple nextflow pipeline for running pangolin
- Host: GitHub
- URL: https://github.com/dfornika/pangolin-simple
- Owner: dfornika
- Created: 2022-12-09T19:54:35.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2022-12-09T20:18:43.000Z (over 2 years ago)
- Last Synced: 2025-01-24T23:48:43.777Z (4 months ago)
- Language: Nextflow
- Size: 1000 Bytes
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# pangolin-simple
A simple nextflow pipeline for running pangolin.
## Usage
```
nextflow run dfornika/pangolin-simple \
-profile conda \
--cache ~/.conda/envs \
--input \
--outdir
```
By default, the pipeline will use pangolin's `accurate` analysis mode (using USHER). The `fast` analysis mode (using PangoLEARN)
can be selected using the `--analysis_mode` flag:
```
nextflow run dfornika/pangolin-simple \
-profile conda \
--cache ~/.conda/envs \
--analysis_mode fast \
--input \
--outdir
```
## Outputs
The pipeline will produce three output files, under the path supplied with the `--outdir` flag:
```
lineage_report.csv
pangolin.stderr.log.txt
pangolin.stdout.log.txt
```