Example Wordcount Package

This is an example workflow package for astrocyte. It contains a worfklow to count the occurences of each word in a text file.

The Workflow

The workflow workflow/main.nf has three processes:

• Convert all the text in the input files to uppercase
• Split the text so each word is on a separate line
• Sort, find and count the occurence of unique words

Parameters

There is a single parameter story. This provides 1 or more files that the workflow should run on.

Containers

The default configuration for this workflow is located in ./workflow/configs/biohpc.config . This configuration will cause the Nextflow command to use the singularity executor for the uppercase, toLines, and wordcount processes, using Docker.io endpoints. The biohpc_*_gitlab.config files show how to instead use images pulled from a specified GitLab repository.

Questions

If you have any questions about this workflow example, or Astrocyte in general, please contact the BioHPC team via biohpc-help@utsouthwestern.edu