# Other Harpy modules

On this page you'll find Harpy functions that aren't standalone workflows. These may create necessary inputs, continue where you left off, or view important workflow files.

Create a template parameter file for the impute module. The file is formatted correctly and serves as a starting point for using parameters that make sense for your study.

harpy imputeparams -o OUTPUTFILE

harpy imputeparams -o params.stitch

Typically, one runs STITCH multiple times, exploring how results vary with different model parameters. The solution Harpy uses for this is to have the user provide a tab-delimited dataframe file where the columns are the 6 STITCH model parameters and the rows are the values for those parameters. To make formatting easier, a template file is generated for you, just replace the values and add/remove rows as necessary. See the section for the impute module for details on these parameters. The template file will look like:

name model	usebx	bxlimit	k	s	ngen
k10_ng50 diploid	TRUE	50000	3	2	10
k1_ng30 diploid	TRUE	50000	3	1	5
high_ngen   diploid TRUE    50000   15  1   100

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. config.yaml), you can use harpy resume . using resume also skips all input validations.

harpy resume [--conda] DIRECTORY

The DIRECTORY is the output directory of a previous harpy-invoked workflow, which must have the workflow/config.yaml file. 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.

Creates a sample grouping file for variant calling

harpy popgroup -o OUTPUTFILE INPUTS

harpy popgroup -o samples.groups data/

This optional file is useful if you want SNP variant calling to happen on a per-population level via harpy snp or on samples pooled-as-populations via harpy sv .

• takes the format of sample tab group
• all the samples will be assigned to group pop1 since file names don't always provide grouping information
  • so make sure to edit the second column to reflect your data correctly.
• the file will look like:

sample1 pop1
sample2 pop1
sample3 pop2
sample4 pop1
sample5 pop3

This convenience command lets you view the latest workflow log file of a Harpy output directory. Use --snakefile or --config to view the workflow snakefile or config.yaml file instead, respectively. Output is printed to the screen via less and accepts the typical keyboard shortcuts to navigate the output.

harpy view [-s] [-c] DIRECTORY

harpy view Align/bwa