dolphinnext/dcrispr repository overview

⁠Running the pipeline

The typical command for running the pipeline is as follows:

nextflow run dolphinnext/dcrispr:1.0 --profile docker --reads '*_R{1,2}.fastq.gz' --mate 'pair'

This will launch the pipeline with the docker configuration profile. See below for more information about profiles.

Note that the pipeline will create the following files in your working directory:

work            # Directory containing the nextflow working files
results         # Finished results 
.nextflow_log   # Log file from Nextflow

⁠Updating the pipeline

When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version. In order to download latest version of the pipeline you need to run followi ng command:

nextflow pull dolpinnext/dcrispr:1.0