inner_read_group_to

inner_read_group_to_string

Converts a ReadGroup struct to a String without any validation.

WDL Version

1.1

RUN WITH

sprocket run --name inner_read_group_to_string data_structures/read_group.wdldata_structures\read_group.wdl [INPUTS]...

Please use the read_group_to_string workflow, which has validation of the ReadGroup contents.

Inputs

Required Inputs

Name

Type

Description

read_group

ReadGroup

ReadGroup struct to stringify

Other Inputs

Name

Type

Default

Description

format_as_sam_record

Boolean

false

Format the `ReadGroup` as a SAM record? If `true`, the read group string will be...

Format the ReadGroup as a SAM record? If true, the read group string will be prefixed with @RG and tab delimiters will be used instead of space delimiters.

false

Outputs

Name

Type

Expression

Description

stringified_read_group

String

read_string("out.txt")

Input ReadGroup as a string

read_string("out.txt")

Default Runtime Attributes

Attribute

Value

memory

"4 GB"

disks

"10 GB"

container

"ghcr.io/stjudecloud/util:2.2.1"

maxRetries

1

Command

if ~{format_as_sam_record}; then echo -n "@RG~{delimiter}" > out.txt fi { echo -n "~{"ID:~{read_group.ID}"}" # required field. All others optional # if any individual placeholder of an interpolated String evaluates to None # the entire parent String will evaluate to the empty String. echo -n "~{"~{delimiter}BC:~{read_group.BC}"}" echo -n "~{"~{delimiter}CN:~{read_group.CN}"}" echo -n "~{"~{delimiter}DS:~{read_group.DS}"}" echo -n "~{"~{delimiter}DT:~{read_group.DT}"}" echo -n "~{"~{delimiter}FO:~{read_group.FO}"}" echo -n "~{"~{delimiter}KS:~{read_group.KS}"}" echo -n "~{"~{delimiter}LB:~{read_group.LB}"}" echo -n "~{"~{delimiter}PG:~{read_group.PG}"}" echo -n "~{"~{delimiter}PI:~{read_group.PI}"}" echo -n "~{"~{delimiter}PL:~{read_group.PL}"}" echo -n "~{"~{delimiter}PM:~{read_group.PM}"}" echo -n "~{"~{delimiter}PU:~{read_group.PU}"}" echo "~{"~{delimiter}SM:~{read_group.SM}"}" } >> out.txt