How to set parameters in a file

It can be useful to store workflow parameters in a file if you’re running complex jobs or you want to keep track of exactly what type of analysis you did.

Make YAML file

Parameters can be stored in YAML format, for example:

input: path/to/samplesheet.csv
pgs_id: 'PGS001229,PGS000018'
liftover: true
target_build: GRCh37

Save this file as my_example_params.yaml. An example template used in pgsc_calc’s test suite is also available.

Run pgsc_calc with YAML file

$ nextflow run pgscatalog/pgsc_calc \
    -profile <conda/docker/singularity> \
    -params-file my_example_params.yaml

The workflow will now run with the parameters you set up in YAML. See Reference: Workflow parameters for a full description of parameters you can set.

Note

If you prefer JSON, you can convert the YAML to JSON and it should work fine