Replacing tab with spaces

[Arun-George-Zachariah]

Changes are done for the below error

Error log:

[info] BackgroundConfigAsyncJobExecutionActor [26437789RNAseq.StarGenerateReferences:NA:1]: Status change from WaitingForReturnCodeFile to Done
[error] WorkflowManagerActor Workflow 26437789-89fc-4174-bba0-98e08f16191f failed (during ExecutingWorkflowState): Job RNAseq.gtfToCallingIntervals:NA:1 exited with return code -1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.
Check the content of stderr for potential additional information: /mydata/gatk-workflows/cromwell-executions/RNAseq/26437789-89fc-4174-bba0-98e08f16191f/call-gtfToCallingIntervals/execution/stderr.
 Could not retrieve content: gatk-workflows/cromwell-executions/RNAseq/26437789-89fc-4174-bba0-98e08f16191f/call-gtfToCallingIntervals/execution/stderr
[info] WorkflowManagerActor WorkflowActor-26437789-89fc-4174-bba0-98e08f16191f is in a terminal state: WorkflowFailedState
[info] SingleWorkflowRunnerActor workflow finished with status 'Failed'.

Error logged in stderr.background:

/cromwell-executions/RNAseq/26437789-89fc-4174-bba0-98e08f16191f/call-gtfToCallingIntervals/execution/script: line 45: warning: here-document at line 19 delimited by end-of-file (wanted `RCODE')
/cromwell-executions/RNAseq/26437789-89fc-4174-bba0-98e08f16191f/call-gtfToCallingIntervals/execution/script: line 46: syntax error: unexpected end of file

[jaavedm]

I am also getting call-gtfToCallingIntervals/execution/script: line 46: syntax error: unexpected end of file error. I made the fix that @Arun-George-Zachariah recommended and the workflow is no longer failing.

[Arun-George-Zachariah]

Thanks, @jaavedm for validating and reconfirming.

[Arun-George-Zachariah]

ReadGroup was added to the workflow to resolve the error The input .bam file contains reads with no platform information that occurs while using BaseRecalibrator

Reference to the error: https://gatk.broadinstitute.org/hc/en-us/community/posts/360056321912-A-USER-ERROR-has-occurred-when-use-the-BaseRecalibrator

@Admin, could you kindly review the need/impact of having ReadGroup?