> 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/multiqc/multiqc_1.10.1.7.md).

# MultiQC v1.10.1.7

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

| Tool    | Version  | Location                                 |
| ------- | -------- | ---------------------------------------- |
| multiqc | 1.10.1.7 | <https://github.com/msk-access/MultiQC/> |

## 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 multiqc.cwl example_inputs.json
```

```bash
#Using CWLTOOL
> cwltool --singularity --non-strict /path/to/multiqc_1.10.1.7/multiqc.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 multiqc.cwl --helpusage: multiqc_1.10.1.cwl [-h]
                          [--qc_files_array_of_array QC_FILES_ARRAY_OF_ARRAY]
                          [--qc_files_dir QC_FILES_DIR]
                          [--qc_list_of_dirs QC_LIST_OF_DIRS]
                          [--report_name REPORT_NAME] [--config CONFIG]
                          [job_order]

Run multiqc on log files from supported bioinformatic tools.

positional arguments:
  job_order             Job input json file

optional arguments:
  -h, --help            show this help message and exit
  --qc_files_array_of_array QC_FILES_ARRAY_OF_ARRAY
                        qc files which shall be part of the multiqc summary;
                        optional, only one of qc_files_array or
                        qc_files_array_of_array must be provided
  --qc_files_dir QC_FILES_DIR
                        qc files in a Directory
  --qc_list_of_dirs QC_LIST_OF_DIRS
                        qc files in multiple directories
  --report_name REPORT_NAME
                        name used for the html report
  --config CONFIG
```