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
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