> 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/picard-tools/picard_add_or_replace_read_groups_2.21.2.md).

# AddOrReplaceReadGroups v2.21.2

## Version of tools in docker image

| Tool   | Version | Location                                                                       |
| ------ | ------- | ------------------------------------------------------------------------------ |
| picard | 2.21.2  | <https://github.com/broadinstitute/picard/releases/download/2.21.2/picard.jar> |

## 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_add_or_replace_read_groups_2.21.2.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_add_or_replace_read_groups_2.21.2/picard_add_or_replace_read_groups_2.21.2.cwl /path/to/inputs.yaml

#Using toil-cwl-runner
> mkdir picardAddOrReplaceReadGroup_toil_log
> toil-cwl-runner --singularity --logFile /path/to/picardAddOrReplaceReadGroup_toil_log/cwltoil.log  --jobStore /path/to/picardAddOrReplaceReadGroup_jobStore --batchSystem lsf --workDir /path/to picardAddOrReplaceReadGroup_toil_log --outdir . --writeLogs /path/to/picardAddOrReplaceReadGroup_toil_log --logLevel DEBUG --stats --retryCount 2 --disableCaching --maxLogFileSize 20000000000 /path/to/picard_add_or_replace_read_groups_2.21.2/picard_add_or_replace_read_groups_2.21.2.cwl /path/to/inputs.yaml > picardAddOrReplaceReadGroup_toil.stdout 2> picardAddOrReplaceReadGroup_toil.stderr &
```

### Usage

```bash
> toil-cwl-runner picard_add_or_replace_read_groups_2.21.2.cwl --help
usage: picard_add_or_replace_read_groups_2.21.2.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         Input file (bam or sam). Required.
  --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}
  --read_group_identifier READ_GROUP_IDENTIFIER
                        Read Group ID Default value: 1. This option can be set
                        to 'null' to clear the default value Required
  --read_group_sequnecing_center READ_GROUP_SEQUNECING_CENTER
                        Read Group sequencing center name Default value: null.
                        Required
  --read_group_library READ_GROUP_LIBRARY
                        Read Group Library. Required
  --read_group_platform_unit READ_GROUP_PLATFORM_UNIT
                        Read Group platform unit (eg. run barcode) Required.
  --read_group_sample_name READ_GROUP_SAMPLE_NAME
                        Read Group sample name. Required
  --read_group_sequencing_platform READ_GROUP_SEQUENCING_PLATFORM
                        Read Group platform (e.g. illumina, solid) Required.
  --read_group_description READ_GROUP_DESCRIPTION
                        Read Group description Default value: null.
  --read_group_run_date READ_GROUP_RUN_DATE
                        Read Group run date Default value: null.
  --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}
```


---

# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.

## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://cmo-ci.gitbook.io/command-line-tools-cwl/develop-1/picard-tools/picard_add_or_replace_read_groups_2.21.2.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.