I am trying to rewrite an RNA-seq pipeline but have been running in problems with Hisat2

My code:

workflow rnaSeq1{
File forwardRead
File reverseRead
Array[File]+ hisat2Index
String Filename
call hisat2_align_tool{
input:
hisat2Index = hisat2Index,
forRead = forwardRead,
revRead = reverseRead,
name = Filename
}
}

task hisat2_align_tool {
Array[File]+ hisat2Index
File forRead
File revRead
String name
runtime {
docker: "kathrinklee/rna-seq-pipeline-hisat2"
}
command <<<
set -e -o pipefail
hisat2 \
-x ~{sub(hisat2Index[0], "\.[0-9]\.ht2", "")} \
-1 ~{forRead} \
-2 ~{revRead} \
-S ~{name}.sam
>>>
output {
File samOut = "${name}.sam"
}
}

my JSON:

{
"rnaSeq1.forwardRead": "data/sample_1.fq",
"rnaSeq1.reverseRead": "data/sample_2.fq",
"rnaSeq1.hisat2Index": [
"reference/index.1.ht2",
"reference/index.2.ht2",
"reference/index.3.ht2",
"reference/index.4.ht2",
"reference/index.5.ht2",
"reference/index.6.ht2",
"reference/index.7.ht2",
"reference/index.8.ht2"],
"rnaSeq1.Filename": "sample"
}

Error log:

[2020-07-13 19:20:02,33] [info] BackgroundConfigAsyncJobExecutionActor [d97600dcrnaSeq1.hisat2_align_tool:NA:1]: Status change from - to Done
[2020-07-13 19:20:02,90] [info] WorkflowManagerActor Workflow d97600dc-2b26-4a9d-9812-6a63f48c37ab failed (during ExecutingWorkflowState): Job rnaSeq1.hisat2_align_tool: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: /home/thinh_vo/WDL-RNAseq/cromwell-executions/rnaSeq1/d97600dc-2b26-4a9d-9812-6a63f48c37ab/call-hisat2_align_tool/execution/stderr.
Could not retrieve content: Could not read from /home/thinh_vo/WDL-RNAseq/cromwell-executions/rnaSeq1/d97600dc-2b26-4a9d-9812-6a63f48c37ab/call-hisat2_align_tool/execution/stderr: /home/thinh_vo/WDL-RNAseq/cromwell-executions/rnaSeq1/d97600dc-2b26-4a9d-9812-6a63f48c37ab/call-hisat2_align_tool/execution/stderr
[2020-07-13 19:20:02,90] [info] WorkflowManagerActor WorkflowActor-d97600dc-2b26-4a9d-9812-6a63f48c37ab is in a terminal state: WorkflowFailedState
[2020-07-13 19:20:11,05] [info] SingleWorkflowRunnerActor workflow finished with status 'Failed'.

cat stderr.background :
/cromwell-executions/rnaSeq1/d97600dc-2b26-4a9d-9812-6a63f48c37ab/call-hisat2_align_tool/execution/script: line 24: syntax error near unexpected token `('
/cromwell-executions/rnaSeq1/d97600dc-2b26-4a9d-9812-6a63f48c37ab/call-hisat2_align_tool/execution/script: line 24: `-x ~{sub(hisat2Index[0], "\.[0-9]\.ht2", "")} \'

what I have tried:

-Copy from cat and past to a new file in case there's a hidden character

-Using WDL plugin on Pycharm to check for syntax error

-Validate with Womtool

please let me know what I miss.