Proof of concept of a DNA-Seq pipeline from reads over VCF to SNP (including quality control) with Nextflow.
- Reads to be mapped must be stored in compressed
.fastq.gz
file format in folderdata
If the reads to be analyzed originate from a human DNA-Seq experiment, this additional file must be stored in folder data
:
- Assembly of the human genome (GRCh38 Genome Reference Consortium Human Reference 38)
hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz
Clone this repository with the following command:
git clone https://github.com/maxgreil/vcftosnp && cd vcftosnp
Then, install Nextflow by using the following command:
curl https://get.nextflow.io | bash
The above snippet creates the nextflow
launcher in the current directory.
Finally pull the following Docker container:
docker pull maxgreil/vcftosnp
Alternatively, you can build the Docker Image yourself using the following command:
cd docker && docker image build . -t maxgreil/vcftosnp
Argument | Usage | Description |
---|---|---|
--reads | <files> | Directory and glob pattern of input files |
--outdir | <folder> | Directory to save output files |
The pipeline is built using Nextflow and processes data using the following steps: