# Resume

When calling a workflow (e.g. qc ), Harpy performs various file checks and validations, sets up the Snakemake command, output folder(s), etc. In the event you want to continue a failed or manually terminated workflow without overwriting the workflow files (e.g. workflow.yaml), you can use harpy resume . Using resume also bypasses all input/argument validations.

usage
harpy resume [--threads] [--direct] DIRECTORY

# arguments

argument	description
`DIRECTORY`	required Output directory of an existing harpy workflow
`--conda`	being deprecated Generate a `/workflow/envs` folder with the necessary conda enviroments
`--direct`	unreleased Launch Snakemake without any Harpy intervention
`--threads`	Change the number of threads the workflow will be run with

The DIRECTORY is the output directory of a previous harpy-invoked workflow, which must have the workflow/config.yaml and workflow/workflow.yaml files. For example, if you previously ran harpy align bwa -o align-bwa ..., then you would use harpy resume align-bwa, which would have the necessary workflow/config.yaml (and other necessary things) required to successfully continue the workflow. Using resume does not overwrite any preprocessing files in the target directory (whereas rerunning the workflow would), which means you can also manually modify the config.yaml file (advanced, not recommended unless you are confident with what you're doing).

resume also requires an existing and populated workdir/envs/ directory in the target directory, like the kind all main harpy workflows would create. If one is not present, you can use --conda to create one (being deprecated).