11  Week 4 Exercises

11.1 In class exercises:

  1. Setup miniwdl to run:
module load cirro
module load Apptainer/1.1.6
export MINIWDL__SCHEDULER__CONTAINER_BACKEND=singularity
  1. Examine scripts/week4/input.json. Run scripts/week4/ww-bwa-samtools.wdl using scripts/week4/input.json (run in bash_for_bio):
miniwdl run -i scripts/week4/input.json scripts/week4/ww-bwa-samtools.wdl

Examine the output directory:

ls -l _LAST/

Look at the outputs:

ls -l _LAST/out
  1. Examine scripts/week4/scatter.json. Run scripts/week4/ww-bwa-samtools-scatter.wdl using scripts/week4/scatter.json
miniwdl run -i scripts/week4/scatter.json scripts/week4/ww-bwa-samtools-scatter.wdl

11.2 Homework Exercises

  • No follow up homework - I suggest you take a look at the WILDS WDL library and identify any tasks you might want to use in your work.
  • Keep an eye out for the Workflows Data Deep Dive next Winter Quarter for more hands-on WDL experience.