# Other Harpy modules

Some parts of Harpy (variant calling, imputation) want or need extra files. You can create various files necessary for different modules using these extra modules:

# Other modules

module	description
`resume`	Continue a Harpy workflow from an existing output folder
`popgroup`	Create generic sample-group file using existing sample file names (fq.gz or bam)
`stitchparams`	Create template STITCH parameter file

# 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. config.yaml), you can use harpy resume .

usage
harpy resume [--conda] DIRECTORY

# arguments

argument	short name	type	default	required	description
`DIRECTORY`		file/directory paths		‼️	Output directory of an existing harpy workflow
`--conda`		toggle			generate a `.harpy_envs/` folder with the necessary conda enviroments

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 .harpy_envs/ directory in the current work directory, like the kind all main harpy workflows would create. If one is not present, you can use --conda to create one.

# popgroup

Creates a sample grouping file for variant calling

usage
harpy popgroup -o OUTPUTFILE INPUTS

usage example
harpy popgroup -o samples.groups data/

# arguments

argument	short name	type	default	required	description
`INPUTS`		file/directory paths		‼️	Files or directories containing input FASTQ/BAM files
`--output`	`-o`	file path		‼️	name of the output file

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:

popgroups.txt
sample1 pop1
sample2 pop1
sample3 pop2
sample4 pop1
sample5 pop3

# stitchparams

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.

usage
harpy stitchparams -o OUTPUTFILE

example
harpy stitchparams -o params.stitch

# arguments

argument	short name	type	default	required	description
`--output`	`-o`	file path		‼️	name of the output file

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:

params.stitch
model	usebx	bxlimit	k	s	ngen
diploid	TRUE	50000	3	2	10
diploid	TRUE	50000	3	1	5