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update with name col
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@pdimens
pdimens committed Nov 11, 2024
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38 changes: 20 additions & 18 deletions Workflows/other.md
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Expand Up @@ -17,20 +17,21 @@ Some parts of Harpy (variant calling, imputation) want or need extra files. You
| `stitchparams` | Create template STITCH parameter file |

### resume
When calling a workflow (e.g. [!badge corners="pill" text="qc"](qc.md)), 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 [!badge corners="pill" text="harpy resume"].
When calling a workflow (e.g. [!badge corners="pill" text="qc"](qc.md)), 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 [!badge corners="pill" text="harpy resume"]. using `resume` also skips all input validations.

```bash usage
harpy resume [--conda] DIRECTORY
```

#### arguments
{.compact}
| 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 |
| argument | short name | type | description |
| :---------- | :--------: | :------------------- | :------------------------------------------------------------------------------------- |
| `DIRECTORY` | | file/directory paths | [!badge variant="info" text="required"] 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`,
Expand All @@ -53,10 +54,10 @@ harpy popgroup -o samples.groups data/
```
#### arguments
{.compact}
| 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 |
| argument | short name | type | description |
| :--------- | :--------: | :------------------- | :-------------------------------------------------------------------------------------------- |
| `INPUTS` | | file/directory paths | [!badge variant="info" text="required"] Files or directories containing input FASTQ/BAM files |
| `--output` | `-o` | file path | [!badge variant="info" text="required"] name of the output file |

This optional file is useful if you want SNP variant calling to happen on a
per-population level via [!badge corners="pill" text="harpy snp"](snp.md/#populations) or on samples
Expand Down Expand Up @@ -87,9 +88,9 @@ harpy stitchparams -o params.stitch

#### arguments
{.compact}
| argument | short name | default | required | description |
| :--------- | :--------: | :-----: | :------: | :---------------------- |
| `--output` | `-o` | | ‼️ | name of the output file |
| argument | short name | description |
| :--------- | :--------: | :-------------------------------------------------------------- |
| `--output` | `-o` | [!badge variant="info" text="required"] 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
Expand All @@ -99,8 +100,9 @@ easier, a template file is generated for you, just replace the values and add/re
rows as necessary. See the section for the [!badge corners="pill" text="impute"](/Workflows/impute.md)
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
```text params.stitch
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
```

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