Nextflow

Runtime

• Fetch a particular version of a pipeline:

Terminal

nextflow pull nf-core/rnaseq -r 3.14.0`

• Hypens:
  • - for Nextflow options
  • -- for pipeline-specific options
    
    
• Find all previous runs in the current directory:

Terminal

nextflow log

Language

• Variables defined by params. can be changed/overridden via command line arguments.

• Every function applied to a channel is a channel operator.

• .flatten() is the opposite of .collect().

• .view() sends to standard output.

Configuration

• Configuration when done within a nextflow script does not require =.

• Configuration when done within a config file requires =.

• Within a config file, whatever is within " and " are expanded. ' can be used if expansion is not desired.