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bcai2 merged 5 commits into from
Nov 2, 2022
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v0.11.2 #285

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7be8b05
fix: logout of ftp connection (#282)
lebovic Oct 28, 2022
68c8049
feat: centrifuge base (#281)
bcai2 Oct 29, 2022
52bade7
chore: fix broken docs links (#283)
bcai2 Oct 31, 2022
8a610c4
chore: add automatic skip for tests on chore commits (#284)
jherr-dev Nov 1, 2022
1cb93e3
chore: bump version
bcai2 Nov 2, 2022
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6 changes: 6 additions & 0 deletions .circleci/config.yml
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Expand Up @@ -38,6 +38,12 @@ jobs:
parallelism: 8
steps:
- checkout
- run:
name: Skip tests if last commit is a chore commit
command: |
cd ~/repo
last_commit="$(git log -1 --pretty=%B | grep chore || true)"
if [ ${#last_commit} -gt 0 ]; then circleci-agent step halt; fi
- run:
name: Create AWS credentials manually
command: |
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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.
110 changes: 110 additions & 0 deletions docs/docs/tool-reference/taxonomic-classifiers/centrifuge.md
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@@ -0,0 +1,110 @@
**Centrifuge** is a rapid and memory-efficient classifier of DNA sequences from microbial samples.
Centrifuge requires a relatively small genome index (e.g., 4.3 GB for ~4,100 bacterial genomes) and can process a
typical DNA sequencing run within an hour. For more information,
see the tool's [website](https://ccb.jhu.edu/software/centrifuge/) and
[GitHub repo](https://github.com/DaehwanKimLab/centrifuge).

Function Call
=============

```python
tc.centrifuge(
output_path=None,
tool_args="",
database_name="centrifuge_refseq_bacteria_archaea_viral_human",
database_version="1",
read_one=None,
read_two=None,
unpaired=None,
is_async=False,
)
```

Function Arguments
------------------

| Argument | Use in place of: | Description |
|:-------------------|:------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| `read_one` | `-1` | (optional) Path(s) to R1 of paired-end read input files. The files can be a local or remote, see [Using Files](../../getting-started/using-files.md). |
| `read_two` | `-2` | (optional) Path(s) to R2 of paired-end read input files. The files can be a local or remote, see [Using Files](../../getting-started/using-files.md). |
| `unpaired` | `-U` | (optional) Path(s) to unpaired input files. The files can be a local or remote, see [Using Files](../../getting-started/using-files.md). |
| `output_path` | output arguments (`-S`, `--report`) | (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 Centrifuge. 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 Centrifuge classification. Defaults to `"centrifuge_refseq_bacteria_archaea_viral_human"` (Refseq bacteria / archaea / viral / human). |
| `database_version` | `-x`\* | (optional) Version of database to use for Centrifuge classification. Defaults to `"1"`. |
| `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.

Output Files
------------

A Centrifuge run will output these files into `output_path`:

- `centrifuge_output.txt`: Centrifuge output (captured from `stdout`), from the `-S` argument.
- `centrifuge_report.tsv`: Centrifuge report file, from the `--report` argument.

Notes
-----

### Paired-end reads

For each paired-end input, make sure the corresponding read is in the same position in the input list. For example, two
pairs of paired-end files – `one_R1.fastq`, `one_R2.fastq`, `two_R1.fastq`, `two_R2.fastq` – should be passed to
Toolchest as:

```python
tc.centrifuge(
read_one=["one_R1.fastq", "two_R1.fastq"],
read_two=["one_R2.fastq", "two_R2.fastq"],
...
)
```

Tool Versions
=============

Toolchest currently supports version **1.0.4** of Centrifuge.

Databases
=========

Toolchest currently supports the following databases for Bowtie 2:

| `database_name` | `database_version` | Description |
|:-------------------------------------------------------| :----------------- |:-------------------------------------------------------------------|
| `centrifuge_refseq_bacteria_archaea_viral_human` | `1` | RefSeq, bacteria / archaea / viral / human, JHU source<sup>1</sup> |

<sup>1</sup>These database indexes were generated by [the Langmead Lab at Johns Hopkins](https://langmead-lab.org/) and can be found on [the lab's database index page](https://benlangmead.github.io/aws-indexes/centrifuge).

Supported Additional Arguments
==============================

Most additional arguments not related to input, output, or multithreading are supported:
- \-q
- \--qseq
- \-f
- \-r
- \-c
- \-s, \--skip
- \-u, \--upto
- \-5, \--trim5
- \-3, \--trim3
- \--phred33
- \--phred64
- \--int-quals
- \--ignore-quals
- \--nofw
- \--norc
- \--min-hitlen
- \-k
- \--host-taxids
- \--exclude-taxids
- \--out-fmt
- \--tab-fmt-cols
- \-t, \--time
- \--qc-filter
- \--seed
- \--non-deterministic

Additional arguments can be specified under the `tool_args` argument.
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