diff --git a/Workflows/other.md b/Workflows/other.md index 6cce57906..08be3f705 100644 --- a/Workflows/other.md +++ b/Workflows/other.md @@ -17,9 +17,10 @@ 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 @@ -27,10 +28,10 @@ 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`, @@ -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 @@ -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 @@ -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 ``` \ No newline at end of file