# Manta v1.5.1
## Version of tools in docker image (/container/Dockerfile)
| Tool | Version | Location |
| ----------------- | ------- | --------------------------------------------------------- |
| ubuntu base image | 16.04 | - |
| manta | 1.5.1 | |
| samtools | 1.9 | |
| htslib | 1.9 | " |
[](https://microbadger.com/images/mskaccess/manta:0.0.2)[](https://microbadger.com/images/mskaccess/manta:0.0.2) [](https://microbadger.com/images/mskaccess/manta:0.0.2) [](https://microbadger.com/images/mskaccess/manta:0.0.2)
## 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 manta_1.5.1.cwl example_inputs.yaml
```
**If at MSK, using the JUNO cluster you can use the following command**
```bash
#Using CWLTOOL
> cwltool --singularity --non-strict /path/to/manta_1.5.1/manta_1.51.cwl /path/to/inputs.yaml
#Using toil-cwl-runner
> mkdir toil_log
> toil-cwl-runner --singularity --logFile /path/to/toil_log/cwltoil.log --jobStore /path/to/jobStore --batchSystem lsf --workDir /path/to =toil_log --outdir . --writeLogs /path/to/toil_log --logLevel DEBUG --stats --retryCount 2 --disableCaching --maxLogFileSize 20000000000 /path/to/manta_1.5.1/manta.1.5.1.cwl /path/to/inputs.yaml > toil.stdout 2> toil.stderr &
```
### Usage
```bash
> toil-cwl-runner manta_1.5.1.cwl --help
usage: manta_1.5.1.cwl [-h]
positional arguments:
job_order Job input json file
optional arguments:
-h, --help show this help message and exit
--memory_per_job MEMORY_PER_JOB
Memory per job in megabytes
--memory_overhead MEMORY_OVERHEAD
Memory overhead per job in megabytes
--number_of_threads NUMBER_OF_THREADS
--call_regions CALL_REGIONS
bgzip-compressed, tabix-indexed BED file specifiying
regions to which variant analysis will be restricted
--non_wgs toggles on settings for WES
--normal_bam NORMAL_BAM
Normal sample BAM or CRAM file. May be specified more
than once, multiple inputs will be treated as each BAM
file representing a different sample. [optional] (no
default)
--output_contigs if true, outputs assembled contig sequences in final
VCF files, in the INFO field CONTIG
--reference_fasta REFERENCE_FASTA
samtools-indexed reference fasta file [required]
--tumor_bam TUMOR_BAM
Tumor sample BAM or CRAM file. Only up to one tumor
bam file accepted.
--generateEvidenceBam
Generate a bam of supporting reads for all SVs
```
---
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