> 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/postprocessing_variant_calls/maf_annotated_by_bed_0.2.2.md).

# maf\_annotated\_by\_bed\_0.2.2

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

| Tool                           | Version | Location                                                |
| ------------------------------ | ------- | ------------------------------------------------------- |
| postprocessing\_variant\_calls | 0.2.3   | ghcr.io/msk-access/postprocessing\_variant\_calls:0.2.3 |

## CWL

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

```bash
    > toil-cwl-runner maf_annotated_by_bed.cwl example_inputs.yaml
```

**If at MSK, using the JUNO cluster having installed toil version 3.19 and manually modifying** [**lsf.py**](https://github.com/DataBiosphere/toil/blob/releases/3.19.0/src/toil/batchSystems/lsf.py#L170) **by removing `type==X86_64 &&` you can use the following command**

```bash
#Using CWLTOOL
> cwltool --singularity --non-strict /path/to/maf_annotated_by_bed.cwl /path/to/inputs.yaml

#Using toil-cwl-runner
> mkdir mafAnnotation_toil_log
> toil-cwl-runner --singularity --logFile /path/to/mafAnnotation_toil_log/cwltoil.log  --jobStore /path/to/mafAnnotation_jobStore --batchSystem lsf --workDir /path/to/mafAnnotation_toil_log --outdir . --writeLogs /path/to/mafAnnotation_toil_log --logLevel DEBUG --stats --retryCount 2 --disableCaching --maxLogFileSize 20000000000 /path/to/maf_annotated_by_bed.cwl /path/to/inputs.yaml > mafAnnotation_toil.stdout 2> mafAnnotation_toil.stderr &
```

### Usage

```shell
usage: maf_annotated_by_bed.cwl
       [-h] [--memory_per_job MEMORY_PER_JOB]
       [--memory_overhead MEMORY_OVERHEAD]
       [--number_of_threads NUMBER_OF_THREADS]
       --input_maf INPUT_MAF
       --input_bed INPUT_BED
       [--output_filename OUTPUT_FILENAME]
       [--column_name COLUMN_NAME]
       [job_order]
```