> For the complete documentation index, see [llms.txt](https://cmo-ci.gitbook.io/command-line-tools-cwl/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://cmo-ci.gitbook.io/command-line-tools-cwl/develop-1/access_utils/0.1.1.md).

# 0.1.1

## Version of tools in docker image (/container/Dockerfile)

| Tool          | Version | Location                                      |
| ------------- | ------- | --------------------------------------------- |
| access\_utils | 0.1.1   | <https://github.com/msk-access/access_utils/> |

## CWL

* CWL specification 1.0
* Use example\_inputs.json to see the inputs to the cwl
* Example Command using [toil](https://toil.readthedocs.io):

```bash
    > toil-cwl-runner general_stats_parse.cwl example_inputs.json
```

```bash
#Using CWLTOOL
> cwltool --singularity --non-strict /path/to/general_stats_parse.cwl /path/to/example_inputs.json

#Using toil-cwl-runner
> mkdir tool_toil_log
> toil-cwl-runner --singularity --logFile /path/to/tool_toil_log/cwltoil.log  --jobStore /path/to/tool_jobStore --batchSystem lsf --workDir /path/to/tool_toil_log --outdir . --writeLogs /path/to/tool_toil_log --logLevel DEBUG --stats --retryCount 2 --disableCaching --maxLogFileSize 20000000000 /path/to/multiqc_1.10.1/multiqc_1.10.1.cwl /path/to/example_inputs.json > tool_toil.stdout 2> tool_toil.stderr &
```

### Usage

```bash
> toil-cwl-runner general_stats_parse.cwl -h
```