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 --entrypoint 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?

false

If true, the read group string will be prefixed with @RG and tab escape sequence (\t) delimiters will be used instead of space delimiters.

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

container

"ghcr.io/stjudecloud/util:3.0.1"

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 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