Run Snippy with Nextflow and containers (Docker or Singularity)
Snippy Code: https://github.com/tseemann/snippy
Snippy Docker file: https://hub.docker.com/r/staphb/snippy/dockerfile
git clone https://github.com/oxfordfun/FunSnippy docker pull docker pull staphb/snippy:4.4.5 singularity build snippy-4.4.5.img docker:https://staphb/snippy:4.4.5
- Reference (Genbank) file, e.g. /data/snippy/H37rV_v3.gbk
- Sequence Reads (paried fastqs), e.g. tests/input/ (input folder)
nextflow run snippy.nf -profile docker \
--input_dir tests/input/ \
--pattern "*_R{1,2}_001.fastq.gz" \
--output_dir tests/output nextflow run snippy.nf -profile singularity \
--input_dir tests/input/ \
--pattern "*_R{1,2}_001.fastq.gz" \
--output_dir tests/output