The pyrpipe_diagnostic command allows users to easily examine pyrpipe logs. It provides several options.

  1. report: This command can generate a summary or detailed report of the analysis.
  2. shell: This command creates a bash file containing all the commands executed via pyrpipe
  3. benchmark: This command can generate benchmarks to compare walltimes of the different commands in the pipeline.
  4. multiqc: This command uses the MultiQC tool to generate a report using pyrpipe logs and other logs geenrated by the pipeline.