get_read_groups
Gets read group information from a BAM file and writes it out as JSON which is converted to a WDL struct.
WDL Version
1.1
RUN WITH
sprocket run --entrypoint get_read_groups data_structures/read_group.wdldata_structures\read_group.wdl [INPUTS]...
This task will uppercase any lowercase PL values it finds, as is required by the SAM specification.
Inputs
Required Inputs
Name
Type
Description
bamFileInput BAM format file to get read groups from
Input BAM format file to get read groups from
Other Inputs
Name
Type
Default
Description
modify_disk_size_gbInt0Add to or subtract from dynamic disk space allocation. Default disk size is determined by the size of the inputs. Specified in GB.
Add to or subtract from dynamic disk space allocation. Default disk size is determined by the size of the inputs. Specified in GB.
Outputs
Name
Type
Expression
Description
read_groupsArray[ReadGroup]read_json("read_groups.json")An array of
ReadGroup structs containing read group information.An array of
ReadGroup structs containing read group information.Default Runtime Attributes
Attribute
Value
disks"~{disk_size_gb} GB"container"ghcr.io/stjudecloud/util:3.0.1"maxRetries1