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.


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