This is a template for a minimal nextflow pipeline that can be used instead of manually submitting a jobfile to SGE for many input files. It contains a lot of instructions and explanations for novice nextflow users and can easily be adapted to more complex pipelines as the project grows.
bin/ # contains custom scripts that are executed from the pipeline
tests/ # contains test files for this example, can be deleted down the road
main.nf # the main workflow definition
nextflow.config # configurations for the workflow and individual processes
run_pipeline.sh # helper script to actually execute the pipeline with environment specific options
Browse through the files, read the comments and adapt them for your needs.
To execute the pipeline, adjust the run_pipeline.sh script and exeute it using
./run_pipeline.sh