star_align failed due to global variable assignment

[akhileshmishra0908]

Hi,
I am getting this error while I am running the example file, may you please help me in this,

(clinker) akhileshmishra@x86_64-apple-darwin13 Clinker-1.32 % bpipe -p out=/Users/akhileshmishra/Documents/Clinker/Clinker-1.32/run -p caller=$CLINKERDIR/test/caller/bcr_abl1.csv -p col=1,2,3,4 -p genome=19 -p print=true -p competitive=true -p header=true -p align_mem=31025992405 -p genome_mem=31025992405 -p fusions=BCR:ABL1 $CLINKERDIR/workflow/clinker.pipe $CLINKERDIR/test/fastq/*.fastq.gz
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| Starting Pipeline at 2022-04-04 19:23 |
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======================================== Stage generate_fst ========================================

====================================== Stage star_genome_gen =======================================

===================================== Stage star_align (test) ======================================
ERROR: stage star_align failed:

 An attempt was made to assign to global variable files after your pipeline already 
 started running. To ensure thread safety, global variables may only be assigned 
 before the pipeline starts. Solutions include:

  - add 'def', 'var', or 'requires' before this assignment to define a local variable,
    eg: def files = "/Users/akhileshmishra/Documents/Clinker/Clinker-1.32/test/fastq/test_R1.fastq.gz /Users/akhileshmishra/Documents/Clinker/Clinker-1.32/test/fastq/test_R2.fastq.gz" or: var files : "/Users/akhileshmishra/Documents/Clinker/Clinker-1.32/test/fastq/test_R1.fastq.gz /Users/akhileshmishra/Documents/Clinker/Clinker-1.32/test/fastq/test_R2.fastq.gz"
  - define a branch variable using: branch.files = "/Users/akhileshmishra/Documents/Clinker/Clinker-1.32/test/fastq/test_R1.fastq.gz /Users/akhileshmishra/Documents/Clinker/Clinker-1.32/test/fastq/test_R2.fastq.gz"

 You can disable this behavior at your own risk by setting allowGlobalWrites=true in 
 your bpipe.config file.

========================================= Pipeline Failed ==========================================

In stage Unknown: One or more parallel stages aborted. The following messages were reported:

-------------------------------------- star_align ( test ) ---------------------------------------

 An attempt was made to assign to global variable files after your pipeline already 
 started running. To ensure thread safety, global variables may only be assigned 
 before the pipeline starts. Solutions include:

  - add 'def', 'var', or 'requires' before this assignment to define a local variable,
    eg: def files = "/Users/akhileshmishra/Documents/Clinker/Clinker-1.32/test/fastq/test_R1.fastq.gz /Users/akhileshmishra/Documents/Clinker/Clinker-1.32/test/fastq/test_R2.fastq.gz" or: var files : "/Users/akhileshmishra/Documents/Clinker/Clinker-1.32/test/fastq/test_R1.fastq.gz /Users/akhileshmishra/Documents/Clinker/Clinker-1.32/test/fastq/test_R2.fastq.gz"
  - define a branch variable using: branch.files = "/Users/akhileshmishra/Documents/Clinker/Clinker-1.32/test/fastq/test_R1.fastq.gz /Users/akhileshmishra/Documents/Clinker/Clinker-1.32/test/fastq/test_R2.fastq.gz"

 You can disable this behavior at your own risk by setting allowGlobalWrites=true in 
 your bpipe.config file.

---

Use 'bpipe errors' to see output from failed commands.

Looking forward for your support.

AKhilesh Mishra
[email protected]