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You need to have nextflow installed, independently of the singularity container, so that nextflow is in your $PATH. ie running just the command nextflow works. Then run:

nextflow run nextflow/variant_call.nf \
    -with-singularity clockwork_container.img 
    ... etc

where you'll have to replace clockwork_container.img with the name that you used when making the container when running singularity build. And the full command as in the wiki page https://github.com/iqbal-lab-org/clockwork/wiki/Pipelines-without-a-database

from clockwork.