Profiles

To select one or multiple profiles, please use the -profile option. For example:

$>  nextflow run scilus/nf-mouse_flow --input input_folder -profile singularity --atlas atlas_directory -resume

Profiles available

singularity

When this profile is used, MouseFlow will use Singularity containers.

docker

When this profile is used, MouseFlow will use Docker containers.

run_preqc

When this profile is used, MouseFlow will run the preqc step. Combined with –use_preqc, it will run the preqc step and use the preqc results to run the pipeline.