Skip to content
Snippets Groups Projects
Peng Lian's avatar
10787f8c

Example Wordcount Package

Build Status Astrocyte

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

Astrocyte workflow containers

The workflow_containers section in astrocyte_pkg.yml defines the URL of the contianers used by this workflow. When the astrocyte_cli run this workflow, it will pull the images in this section and save them to workflow/images/singularity/ for later use.
In the workflow, the default configuration located in workflow/configs/biohpc.config defines how the Nextflow command to use the singularity executor for the uppercase, toLines, and wordcount processes.

Vizapp containers

The astrocyte_cli version 2.0.0 supports containerized vizapp, so that vizapp becomes more independent and can be run on multiple platforms. The astrocyte workflow developers do not need to change their vizapp_* settings in astrocyte_pkg.yml to use this feature. The shiny-prepare command with the --with-container option will pull the right version of R container from the BioHPC "Astrocyte Container Images" registry and save it to the vizapp folder for later use. Also, it will create a folder vizapp/.rlibrary to install the dependencies pacages.

Questions

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