This folder contains the workflow design files for the nextflow workflows.
The respective main workflow files are the *.nf files, however you may need additional input and configuration files which might also need adjustment to your infrastructure, found in the inputs folder, for more details see [below](## Documentation). Workflow execution will also depend on the availability of the containers, read on in the documentation and [below](## Documentation).
The documentation helpful for technical aspects of the workflow execution are in the docs folder.
Singularity container definition files referenced in the workflow configuration file can be found in the container folder. Brief build instructions can also be found there, for more see the documentation.
./nextflow run pridereswath.nf -params-file pridereswath.yaml -c nf.config --irtkit /fs/irt.TraML --lib /fs/library.tsv --wiff /fs/input/ --out_dir /fs/output/