NextFlow pipeline for SARS-CoV-2 Illumina data

This pipeline is reimplementation of pzh_pipeline_sars_illumina in NextFlow. I has also integrated SV module from pzh_pipeline_sars_illumina_SV.

For installation and usage vide doc/pdfSourceDOC.pdf

Name		Name	Last commit message	Last commit date
Latest commit History 67 Commits
bin		bin
data		data
doc		doc
modules		modules
third-party		third-party
.dockerignore		.dockerignore
.gitignore		.gitignore
Dockerfile-main		Dockerfile-main
Dockerfile-manta		Dockerfile-manta
README.md		README.md
flowchart-raw.png		flowchart-raw.png
flowchart.dot		flowchart.dot
flowchart.png		flowchart.png
nextflow.config		nextflow.config
nf_pipeline.nf		nf_pipeline.nf
requirements.txt		requirements.txt
run_nf_pipeline.sh		run_nf_pipeline.sh
update_external_databases.sh		update_external_databases.sh

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