GPSC Pipeline

Quick start

Installation

GBS Typer relies on Nextflow and Docker. Download:

1. Docker.
2. Nextflow.
3. Clone repository:

git clone https://github.com/sanger-bentley-group/GPSC_pipeline_nf.git
cd GPSC_pipeline_nf

Run pipeline

nextflow run main.nf --manifest your_manifest.txt --results_dir results

Your manifest your_manifest.txt must be a tab-delimited file with headers sample_id and assembly, e.g.

sample_id	assembly
sample1	/location/of/assembly/file1.fa
sample2	/location/of/assembly/file2.fa

The first time you run the pipeline, it will download the GPS_v6 database in a db directory (within the current directory where you run the pipeline). If you would like to use an existing GPS_v6 database instead (and not re-download it), create a directory called db and move/symlink your GPS_v6 database.

Output

csv file gps_output.csv in results_dir, e.g.:

Taxon,Cluster,db_version
12291_4#66,1,GPS_v6
12291_4#65,1,GPS_v6
12291_4#69,1,GPS_v6

Test pipeline

This test checks whether the output is expected.

./tests/regression_tests.sh