Every nf-core pipeline repository should contain a single pipeline. That is, there should be a main.nf file that is the single way to launch a pipeline.

  • It is ok to have multiple ‘tracks’ within the pipeline, selectable with configuration options.
  • It is ok to have workflows that use the output of another nf-core pipeline as input

It should be possible to run all parts of the workflow using nextflow run nf-core/<pipeline>, without any specific filename.