chore: fix broken docs links (#283)

bcai2 · web-flow · commit 52bade724d35 · 2022-10-31T14:01:31.000-07:00
diff --git a/README.md b/README.md
@@ -29,7 +29,7 @@ toolchest.kraken2(
 )
 ```
 
-For a list of available tools, see the [documentation](https://docs.trytoolchest.com/docs#-tools).
+For a list of available tools, see the [documentation](https://docs.trytoolchest.com/tool-reference/about/).
 
 ## Configuration
 
diff --git a/docs/docs/tool-reference/aligners/bowtie-2.md b/docs/docs/tool-reference/aligners/bowtie-2.md
@@ -21,7 +21,7 @@ Function Arguments
 | :----------------- | :------------------ | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | `inputs`           | `-U`                | Path to one or more files to use as input. The files can be a local or remote, see [Using Files](../../getting-started/using-files.md).                                                                                          |
 | `output_path`      | `-S`                | (optional) Path (directory) to where the output files will be downloaded. If omitted, skips download. The files can be a local or remote, see [Using Files](../../getting-started/using-files.md).                               |
-| `tool_args`        | all other arguments | (optional) Additional arguments to be passed to Bowtie 2. This should be a string of arguments like the command line. See [Supported Additional Arguments](https://docs.trytoolchest.com/docs/bowtie-2#supported-additional-arguments) for more details. |
+| `tool_args`        | all other arguments | (optional) Additional arguments to be passed to Bowtie 2. This should be a string of arguments like the command line. See [Supported Additional Arguments](#supported-additional-arguments) for more details. |
 | `database_name`    | `-x`\*              | (optional) Name of database to use for Bowtie 2 alignment. Defaults to `"GRCh38_noalt_as"` (human genome).                                                                                                                                               |
 | `database_version` | `-x`\*              | (optional) Version of database to use for Bowtie 2 alignment. Defaults to `"1"`.                                                                                                                                                                         |
 | `is_async`         |                     | Whether to run a job asynchronously.  See [Async Runs](../../feature-reference/async-runs.md) for more.                                                                                                                                                                  |
diff --git a/docs/docs/tool-reference/aligners/clustal-omega.md b/docs/docs/tool-reference/aligners/clustal-omega.md
@@ -22,7 +22,7 @@ See the Notes section below for more details.
 | :------------ | :------------------ | :----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | `inputs`      | `-i`                | Path to one or more files to use as input. The files can be a local or remote, see [Using Files](../../getting-started/using-files.md).                                                                                                    |
 | `output_path` | `-o`                | (optional) Path (directory) to where the output files will be downloaded. If omitted, skips download. The files can be a local or remote, see [Using Files](../../getting-started/using-files.md).                                         |
-| `tool_args`   | all other arguments | (optional) Additional arguments to be passed to Clustal Omega. This should be a string of arguments like the command line. See [Supported Additional Arguments](https://docs.trytoolchest.com/docs/clustal-omega#supported-additional-arguments) for more details. |
+| `tool_args`   | all other arguments | (optional) Additional arguments to be passed to Clustal Omega. This should be a string of arguments like the command line. See [Supported Additional Arguments](#supported-additional-arguments) for more details. |
 | `is_async`    |                     | Whether to run a job asynchronously.  See [Async Runs](../../feature-reference/async-runs.md) for more.                                                                                                                                                                            |
 
 Tool Versions
diff --git a/docs/docs/tool-reference/aligners/rapsearch2.md b/docs/docs/tool-reference/aligners/rapsearch2.md
@@ -21,14 +21,14 @@ Function Arguments
 
 See the Notes section below for more details.
 
-| Argument           | Use in place of:    | Description                                                                                                                                                                                                                                                   |
-| :----------------- | :------------------ | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
-| `inputs`           | `-q`                | Path to one or more files to use as input. The files can be a local or remote, see [Using Files](../../getting-started/using-files.md).                                                                                               |
-| `output_path`      | `-o`                | (optional) Path (directory) to where the output files will be downloaded. If omitted, skips download. The files can be a local or remote, see [Using Files](../../getting-started/using-files.md).                                    |
-| `database_name`    | `-d`\*              | (optional) Name of database to use for RAPSearch2 alignment. Defaults to `"GRCh38"` (human genome).                                                                                                                                                           |
-| `database_version` | `-d`\*              | (optional) Version of database to use for RAPSearch2 alignment. Defaults to `"1"`.                                                                                                                                                                            |
-| `tool_args`        | all other arguments | (optional) Additional arguments to be passed to RAPSearch2. This should be a string of arguments like the command line. See [Supported Additional Arguments](https://docs.trytoolchest.com/docs/rapsearch-2#supported-additional-arguments) for more details. |
-| `is_async`         |                     | Whether to run a job asynchronously.  See [Async Runs](../../feature-reference/async-runs.md) for more.                                                                                                                                                                       |
+| Argument           | Use in place of:    | Description                                                                                                                                                                                                                                                                  |
+| :----------------- | :------------------ |:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| `inputs`           | `-q`                | Path to one or more files to use as input. The files can be a local or remote, see [Using Files](../../getting-started/using-files.md).                                                                                                                                      |
+| `output_path`      | `-o`                | (optional) Path (directory) to where the output files will be downloaded. If omitted, skips download. The files can be a local or remote, see [Using Files](../../getting-started/using-files.md).                                                                           |
+| `database_name`    | `-d`\*              | (optional) Name of database to use for RAPSearch2 alignment. Defaults to `"GRCh38"` (human genome).                                                                                                                                                                          |
+| `database_version` | `-d`\*              | (optional) Version of database to use for RAPSearch2 alignment. Defaults to `"1"`.                                                                                                                                                                                           |
+| `tool_args`        | all other arguments | (optional) Additional arguments to be passed to RAPSearch2. This should be a string of arguments like the command line. See [Supported Additional Arguments](#supported-additional-arguments) for more details.                                                              |
+| `is_async`         |                     | Whether to run a job asynchronously.  See [Async Runs](../../feature-reference/async-runs.md) for more.                                                                                                                                                                      |
 
 \*See the [Databases](#databases) section for more details.
 
diff --git a/docs/docs/tool-reference/assemblers/unicycler.md b/docs/docs/tool-reference/assemblers/unicycler.md
@@ -24,7 +24,7 @@ Function Arguments
 | `read_two`    | `-2`                | (optional) Path to R2 of paired-end short read input files. The file can be a local or remote, see [Using Files](../../getting-started/using-files.md).                                                                            |
 | `long_reads`  | `-l`                | (optional) Path to the file containing long reads. The file can be a local or remote, see [Using Files](../../getting-started/using-files.md).                                                                                     |
 | `output_path` | `-o`                | (optional) Path (directory) to where the output files will be downloaded. If omitted, skips download. The files can be a local or remote, see [Using Files](../../getting-started/using-files.md).                                 |
-| `tool_args`   | all other arguments | (optional) Additional arguments to be passed to Unicycler. This should be a string of arguments like the command line. See [Supported Additional Arguments](https://docs.trytoolchest.com/docs/unicycler#supported-additional-arguments) for more details. |
+| `tool_args`   | all other arguments | (optional) Additional arguments to be passed to Unicycler. This should be a string of arguments like the command line. See [Supported Additional Arguments](#supported-additional-arguments) for more details. |
 | `is_async`    |                     | Whether to run a job asynchronously.  See [Async Runs](../../feature-reference/async-runs.md) for more.                                                                                                                                                                    |
 
 Notes
diff --git a/docs/docs/tool-reference/post-processing/bracken.md b/docs/docs/tool-reference/post-processing/bracken.md
@@ -23,7 +23,7 @@ tc.bracken(
 | `kraken2_report`       | Kraken 2 report file input | Path to Kraken 2 report file. The files can be a local or remote, see [Using Files](../../getting-started/using-files.md).                                                                                                      |
 | `output_path`          | `-o` directory name        | (optional) Path (directory) to where the output files will be downloaded. If omitted, skips download. The files can be a local or remote, see [Using Files](../../getting-started/using-files.md).                              |
 | `output_primary_name`  | `-o` file name             | (Optional) Name of Bracken output file. Defaults to `"output.bracken"`.                                                                                                                                                                                 |
-| `tool_args`            | all other arguments        | (optional) Additional arguments to be passed to Bracken. This should be a string of arguments like the command line. See [Supported Additional Arguments](https://docs.trytoolchest.com/docs/kraken-2#supported-additional-arguments) for more details. |
+| `tool_args`            | all other arguments        | (optional) Additional arguments to be passed to Bracken. This should be a string of arguments like the command line. See [Supported Additional Arguments](#supported-additional-arguments) for more details. |
 | `database_name`        | `-d`                       | (optional) Name of database that was used for Kraken 2 alignment. Defaults to `"standard"`.                                                                                                                                                             |
 | `database_version`     | `-d`                       | (optional) Version of database that was used for Kraken 2 alignment. Defaults to `"1"`.                                                                                                                                                                 |
 | `remote_database_path` | `-d`                       | (optional) AWS S3 URI to a directory with your custom database that was used with Kraken 2 alignment.                                                                                                                                                   |
diff --git a/docs/docs/tool-reference/structure-prediction/alphafold.md b/docs/docs/tool-reference/structure-prediction/alphafold.md
@@ -52,4 +52,4 @@ Toolchest supports the following arguments for AlphaFold:
 - `--max_template_date`
 - `--model_preset`
 
-However, these should be specified via specific argument values in the function call, rather than through a generic `tool_args` argument (like other Toolchest tools). See [Function Arguments](https://docs.trytoolchest.com/docs/alphafold#function-arguments) for more details.
+However, these should be specified via specific argument values in the function call, rather than through a generic `tool_args` argument (like other Toolchest tools). See [Function Arguments](#function-arguments) for more details.
diff --git a/docs/docs/tool-reference/taxonomic-classifiers/kraken-2.md b/docs/docs/tool-reference/taxonomic-classifiers/kraken-2.md
@@ -25,7 +25,7 @@ tc.kraken2(
 | `read_one`             | `--paired`, input file location | (optional) Path to R1 of paired-end read input files. The file can be a local or remote, see [Using Files](../../getting-started/using-files.md).                                                                                |
 | `read_two`             | `--paired`, input file location | (optional) Path to R2 of paired-end read input files. The file can be a local or remote, see [Using Files](../../getting-started/using-files.md).                                                                                |
 | `output_path`          | output file location            | (optional) Path (directory) to where the output files will be downloaded. If omitted, skips download. The files can be a local or remote, see [Using Files](../../getting-started/using-files.md).                               |
-| `tool_args`            | all other arguments             | (optional) Additional arguments to be passed to Kraken 2. This should be a string of arguments like the command line. See [Supported Additional Arguments](https://docs.trytoolchest.com/docs/kraken-2#supported-additional-arguments) for more details. |
+| `tool_args`            | all other arguments             | (optional) Additional arguments to be passed to Kraken 2. This should be a string of arguments like the command line. See [Supported Additional Arguments](#supported-additional-arguments) for more details. |
 | `database_name`        | `--db`                          | (optional) Name of database to use for Kraken 2 alignment. Defaults to `"standard"`.                                                                                                                                                                     |
 | `database_version`     | `-db`                           | (optional) Version of database to use for Kraken 2 alignment. Defaults to `"1"`.                                                                                                                                                                         |
 | `remote_database_path` | `-db`                           | (optional) AWS S3 URI to a directory with your custom database.                                                                                                                                                                                          |

Original file line number	Diff line number	Diff line change
`@@ -29,7 +29,7 @@ toolchest.kraken2(`
`29`	`29`	`)`
`30`	`30`	```
`31`	`31`
`32`		`-For a list of available tools, see the [documentation](https://docs.trytoolchest.com/docs#-tools).`
	`32`	`+For a list of available tools, see the [documentation](https://docs.trytoolchest.com/tool-reference/about/).`
`33`	`33`
`34`	`34`	`## Configuration`
`35`	`35`