# FixMateInformation v1.96

## Version of tools in docker image (../picard\_add\_or\_replace\_read\_groups\_1.96/container/Dockerfile)

| Tool            | Version | Location                                                                                |
| --------------- | ------- | --------------------------------------------------------------------------------------- |
| java base image | 8       | -                                                                                       |
| picard          | 1.96    | <https://sourceforge.net/projects/picard/files/picard-tools/1.96/picard-tools-1.96.zip> |
| R               | 3.3.3   | r-base for opnejdk:8                                                                    |

[![](https://images.microbadger.com/badges/image/mskcc/picard_1.96:0.1.0.svg)](https://microbadger.com/images/mskcc/picard_1.96:0.1.0) [![](https://images.microbadger.com/badges/version/mskcc/picard_1.96:0.1.0.svg)](https://microbadger.com/images/mskcc/picard_1.96:0.1.0) [![](https://images.microbadger.com/badges/license/mskcc/picard_1.96:0.1.0.svg)](https://microbadger.com/images/mskcc/picard_1.96:0.1.0)

## 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 picard_fix_mate_information_1.96.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/picard_fix_mate_information_1.96/picard_fix_mate_information_1.96.cwl /path/to/inputs.yaml

#Using toil-cwl-runner
> mkdir picardFixMate_toil_log
> toil-cwl-runner --singularity --logFile /path/to/picardFixMate_toil_log/cwltoil.log  --jobStore /path/to/picardFixMate_jobStore --batchSystem lsf --workDir /path/to picardFixMate_toil_log --outdir . --writeLogs /path/to/picardFixMate_toil_log --logLevel DEBUG --stats --retryCount 2 --disableCaching --maxLogFileSize 20000000000 /path/to/picard_fix_mate_information_1.96/picard_fix_mate_information_1.96.cwl /path/to/inputs.yaml > picardFixMate_toil.stdout 2> picardFixMate_toil.stderr &
```

### Usage

```
usage: picard_fix_mate_information_1.96.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
  --input INPUT         The input file to fix. This option may be specified 0
                        or more times
  --output_file_name OUTPUT_FILE_NAME
                        Output file name (bam or sam). Not Required
  --sort_order SORT_ORDER
                        Optional sort order to output in. If not supplied
                        OUTPUT is in the same order as INPUT.Default value:
                        null. Possible values: {unsorted, queryname,
                        coordinate}
  --tmp_dir TMP_DIR     This option may be specified 0 or more times
  --validation_stringency VALIDATION_STRINGENCY
                        Validation stringency for all SAM files read by this
                        program. Setting stringency to SILENT can improve
                        performance when processing a BAM file in which
                        variable-length data (read, qualities, tags) do not
                        otherwise need to be decoded. Default value: STRICT.
                        This option can be set to 'null' to clear the default
                        value. Possible values: {STRICT,LENIENT, SILENT}
  --bam_compression_level BAM_COMPRESSION_LEVEL
                        Compression level for all compressed files created
                        (e.g. BAM and GELI). Default value:5. This option can
                        be set to 'null' to clear the default value.
  --create_bam_index    Whether to create a BAM index when writing a
                        coordinate-sorted BAM file. Default value:false. This
                        option can be set to 'null' to clear the default
                        value. Possible values:{true, false}
```


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