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bcai2 merged 1 commit into from
Oct 31, 2022
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chore: fix broken docs links #283

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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -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

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2 changes: 1 addition & 1 deletion docs/docs/tool-reference/aligners/bowtie-2.md
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Expand Up @@ -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. |
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2 changes: 1 addition & 1 deletion docs/docs/tool-reference/aligners/clustal-omega.md
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Expand Up @@ -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
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16 changes: 8 additions & 8 deletions docs/docs/tool-reference/aligners/rapsearch2.md
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Expand Up @@ -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.

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2 changes: 1 addition & 1 deletion docs/docs/tool-reference/assemblers/unicycler.md
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion docs/docs/tool-reference/post-processing/bracken.md
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Expand Up @@ -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. |
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2 changes: 1 addition & 1 deletion docs/docs/tool-reference/structure-prediction/alphafold.md
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Expand Up @@ -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.
2 changes: 1 addition & 1 deletion docs/docs/tool-reference/taxonomic-classifiers/kraken-2.md
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Expand Up @@ -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. |
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