If you are new to developing with this project, the following hints may be useful:
The nextflow_schema.json file contains the list of parameters and their documentation, and is used to automatically generate the Nextflow Tower UI for this pipeline. If you want to change the parameters or their docs, use the nf-core schema builder. Copy and paste the contents of the nextflow_schema.json file into the tool to begin editing, and copy it back when you are done. Don't forget to update the parameter docs, as described below.
To generate the Parameters documentation from the Nextflow schema, first install nf-core tools, and then:
nf-core schema docs -o docs/Parameters.md -f -c parameter,description,type
All containers used by the pipeline have been made available on Docker Hub and AWS ECR. You can rebuild these to make customizations or to replace the algorithms used. To build the containers and push to Docker Hub, install maru and run maru build.
To push to Docker Hub, you need to login first:
docker login
To push to AWS ECR, you need to login as follows:
aws ecr-public get-login-password --region us-east-1 | docker login --username AWS --password-stdin public.ecr.aws