This directory contains a series of bash scripts which automate several tasks which can be used as sample work to test the different capabilities of technical metrics collectors like treecript.

• download-and-test-linux-6.6.bash is a script which fetches content compressed with two different algorithms (in this case, public snapshots of the Linux Kernel source code) to a temporary directory, and tests the integrity of both archives as well as lists their internal contents. It assumes both tar, gunzip and unxz are available.

• download-and-run-nextflow-workflow.bash: This script fetches into a temporary directory both an old variant calling workflow written in Nextflow v1, as well as all its dependencies: a JVM; a capable old nextflow engine; the inputs; the reference datasets; ... Once all is fetched the layout is prepared to be able to run the workflow using the inputs and DBs. It assumes docker is properly setup, up and running for the user using the script.

• download-NXF-and-amplicon-analysis-pipeline.bash and run-downloaded-NXF-and-amplicon-analysis-pipeline.bash: The first bash script fetches to a given input working directory the workflow amplicon-analysis-pipeline v6.0.4, as well as all the input, database and software pre-conditions. Once all the content is fetched, the directories layout expected by the workflow is prepared.

  The second bash script takes as input a working directory already prepared by the previous script, as well as an output directory. This last one will be used to store the results computed by the workflow when it uses the fetched inputs.