NextFlow pipeline for SARS-CoV-2 Nanopore data

This pipeline is reimplementation of pzh_pipeline_sars_nanopore in NextFlow.

Building

DOCKER_BUILDKIT=1 docker build --target main -t nf_nanopore_sars-3.0-main:latest .

You can enter docker with:

docker run -it --rm nf_nanopore_sars-3.0-main:latest

nf-tests test

Name		Name	Last commit message	Last commit date
Latest commit History 35 Commits
.github/workflows		.github/workflows
bin		bin
data		data
modules		modules
testing_data		testing_data
tests		tests
third-party		third-party
.dockerignore		.dockerignore
.gitignore		.gitignore
Dockerfile		Dockerfile
README.md		README.md
flowchart-raw.png		flowchart-raw.png
nextflow.config		nextflow.config
nf-test.config		nf-test.config
nf_pipeline.nf		nf_pipeline.nf
requirements.txt		requirements.txt
run_nf_pipeline.sh.template		run_nf_pipeline.sh.template