update to 1.13

pdimens · Nov 26, 2024 · 9722fe0 · 9722fe0
1 parent 57da1aa
commit 9722fe0
Show file tree

Hide file tree

Showing 4 changed files with 61 additions and 35 deletions.
diff --git a/Workflows/impute.md b/Workflows/impute.md
@@ -44,8 +44,8 @@ harpy impute OPTIONS... INPUTS...
 ```
 
 ```bash example
-# create stitch parameter file 'stitch.params'
-harpy stitchparams -o stitch.params 
+# create the parameter file 'stitch.params'
+harpy imputeparams -o stitch.params 
 
 # run imputation
 harpy impute --threads 20 --vcf Variants/mpileup/variants.raw.bcf --parameters stitch.params Align/ema
@@ -86,7 +86,7 @@ Typically, one runs STITCH multiple times, exploring how results vary with
 different model parameters (explained in next section). 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. The parameter file 
-is required and can be created manually or with [!badge corners="pill" text="harpy stitchparams"](other.md/#stitchparams).
+is required and can be created manually or with [!badge corners="pill" text="harpy imputeparams"](other.md/#imputeparams).
 If created using harpy, the resulting file includes largely meaningless values 
 that you will need to adjust for your study. The parameter must follow a particular format:
 - tab or comma delimited

diff --git a/Workflows/other.md b/Workflows/other.md
@@ -12,9 +12,44 @@ Some parts of Harpy (variant calling, imputation) want or need extra files. You
 {.compact}
 | module         | description                                                                      |
 | :------------- | :------------------------------------------------------------------------------- |
+| `imputeparams` | Create a template imputation parameter file                                      |
 | `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                                            |
+| `view`         | View a workflow log, config, or snakefile                                        |
+
+### imputeparams
+Create a template parameter file for the [!badge corners="pill" text="impute"](/Workflows/impute.md) module. 
+The file is formatted correctly and serves as a starting point for using parameters that make sense for your study.
+
+```bash usage
+harpy imputeparams -o OUTPUTFILE
+```
+
+```bash example
+harpy imputeparams -o params.stitch
+```
+
+#### arguments
+{.compact}
+| 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
+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 [!badge corners="pill" text="impute"](/Workflows/impute.md)
+module for details on these parameters. The template file will look like:
+
+```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
+```
+---
 
 ### resume
 When calling a workflow (e.g. [!badge corners="pill" text="qc"](qc.md)), Harpy performs various file checks
@@ -31,15 +66,15 @@ harpy resume [--conda] DIRECTORY
 | 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                  |
+| `--conda`   |            | toggle               | Generate a `/workflow/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 [!badge corners="pill" text="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).
 
-[!badge corners="pill" text="resume"] also requires an existing and populated `.harpy_envs/` directory in the current work directory, like the kind all
+[!badge corners="pill" text="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.
 
 ### popgroup
@@ -57,7 +92,7 @@ harpy popgroup -o samples.groups data/
 | 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                               |
+| `--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
@@ -74,35 +109,25 @@ sample4 pop1
 sample5 pop3
 ```
 ---
-### stitchparams
-Create a template parameter file for the [!badge corners="pill" text="impute"](/Workflows/impute.md) module. The file is formatted correctly and serves
-as a starting point for using parameters that make sense for your study.
+
+### view
+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](https://gist.github.com/glnds/8862214) the output.
 
 ```bash usage
-harpy stitchparams -o OUTPUTFILE
+harpy view [-s] [-c] DIRECTORY
 ```
 
 ```bash example
-harpy stitchparams -o params.stitch
+harpy view Align/bwa
 ```
 
 #### arguments
 {.compact}
-| 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
-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 [!badge corners="pill" text="impute"](/Workflows/impute.md)
-module for details on these parameters. The template file will look like:
-
-```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
-```
+| argument      | short name | description                                                                            |
+| :------------ | :--------: | :------------------------------------------------------------------------------------- |
+| `DIRECTORY`   |            | [!badge variant="info" text="required"] Output directory of an existing harpy workflow |
+| `--snakemake` |    `-s`    | View the workflow snakefile instead                                                    |
+| `--config`    |    `-c`    | View the `config.yaml` file instead                                                    |
diff --git a/index.md b/index.md
@@ -62,12 +62,13 @@ You can call `harpy` without any arguments (or with `--help`) to print the docst
 │ metassembly  Create a metassembly from linked-reads                     │
 ╰─────────────────────────────────────────────────────────────────────────╯
 ╭─ Other Commands ────────────────────────────────────────────────────────╮
-│ resume        Resume a workflow from an existing Harpy directory        │
-│ hpc           Profile templates for cluster job submissions             │
-│ preflight     File format checks for haplotag data                      │
 │ deconvolve    Resolve clashing barcodes from different molecules        │
+│ hpc           Profile templates for cluster job submissions             │
+│ imputeparams  Create a template imputation parameter file               │
 │ popgroup      Create a template grouping file for samples               │
-│ stitchparams  Create a template STITCH parameter file                   │
+│ preflight     File format checks for haplotag data                      │
+│ resume        Resume a workflow from an existing Harpy directory        │
+│ view          View a workflow log, config, or snakefile                 │
 ╰─────────────────────────────────────────────────────────────────────────╯
 ```
 

diff --git a/retype.yml b/retype.yml
@@ -7,7 +7,7 @@ footer:
   copyright: "&copy; Copyright {{ year }}. All rights reserved."
 branding:
   title: Harpy
-  label: v1.12
+  label: v1.13
   logo: static/logo_navbar.png
   logoDark: static/logo_navbar.png
   logoAlign: left