Is your feature request related to a problem? Please describe.
Defining a container in Pegasus workflows requires an explicit call to a specific engine, such as NAMESPACE.SINGULARITY. This requires lengthy if-else statements and relies on CLI input to support systems with only 1 container engine.
Describe the solution you'd like
The solution could be to keep the Container function description generic with no NAMESPACE call, and let user define the container engine in the NAMESPACE.PEGASUS or add_pegasus_profile with an argument like container='docker', etc.
Additionally, it would be very helpful if the Container function included an option to define separate containers for different container engines. For example, the workflow developer can provide options for Singularity and Docker containers, and depending on the user's selection, the relevant container will be pulled.
Example solution:
site.add_pegasus_profile(container_engine = "singularity")
container = Container(
"alphafold3",
docker = "baldikacti/alphafold3:latest",
singularity = "https://depot.galaxyproject.org/singularity/alphafold3:latest",
)
Is your feature request related to a problem? Please describe.
Defining a container in Pegasus workflows requires an explicit call to a specific engine, such as
NAMESPACE.SINGULARITY. This requires lengthy if-else statements and relies on CLI input to support systems with only 1 container engine.Describe the solution you'd like
The solution could be to keep the
Containerfunction description generic with noNAMESPACEcall, and let user define the container engine in theNAMESPACE.PEGASUSoradd_pegasus_profilewith an argument likecontainer='docker', etc.Additionally, it would be very helpful if the
Containerfunction included an option to define separate containers for different container engines. For example, the workflow developer can provide options for Singularity and Docker containers, and depending on the user's selection, the relevant container will be pulled.Example solution: