# bcftools tabix v1.15.1

### CWL and Docker for Running tabs using bcftools v1.15.1

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

| Tool     | Version | Location                                                   |
| -------- | ------- | ---------------------------------------------------------- |
| bcftools | 1.15.1  | <https://github.com/samtools/bcftools/releases/tag/1.15.1> |

### CWL

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

```
toil-cwl-runner bcftools_tabix_1.15.1.cwl example_input_tabix.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**

```shell
#Using CWLTOOL
cwltool --singularity --non-strict /path/to/bcftools_tabix_1.15.1.cwl /path/to/inputs.yaml

#Using toil-cwl-runner
mkdir bcftools_toil_log
toil-cwl-runner --singularity --logFile /path/to/bcftools_toil_log/cwltoil.log  --jobStore /path/to/bcftools_jobStore --batchSystem lsf --workDir /path/to/bcftools_toil_log --outdir . --writeLogs /path/to/bcftools_toil_log --logLevel DEBUG --stats --retryCount 2 --disableCaching --maxLogFileSize 20000000000 /path/to/bcftools_tabix_1.15.1.cwl /path/to/inputs.yaml > bcftools_toil.stdout 2> bcftools_toil.stderr &
```

#### Usage

```shell
usage: bcftools_tabix_1.15.1.cwl [-h] 

positional arguments:
  job_order      Job input json file

optional arguments:
  -h, --help     show this help message and exit
  --input INPUT  input VCF file
```


---

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