Building CWL tools for BadGenomicsKmers


I am getting error while running newly build CWL tool for BadGenomicsKmers.

CWL tools is below.

#!/usr/bin/env cwl-runner

# This tool description was generated automatically by wdl2cwl ver. 0.2

class: CommandLineTool

cwlVersion: v1.0


- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
- class: InitialWorkDirRequirement
    - $(inputs.ReferenceGenome)


- id: ReferenceGenome

  type: File

- id: ReferenceGenomeDict

  type: File

- id: sampleName

  type: string


- id: kmers_to_ignore

  type: File


    glob: $(inputs.sampleName).txt

baseCommand: []


- valueFrom: |-

    gatk FindBadGenomicKmersSpark -R $(inputs.ReferenceGenome.path) -O $(inputs.sampleName).txt

  shellQuote: false

Generated error is as follows.

10:00:10.659 INFO  FindBadGenomicKmersSpark - Shutting down engine
[May 28, 2020 10:00:10 AM GMT] done. Elapsed time: 0.22 minutes.

A USER ERROR has occurred: Fasta dict file for reference /ySLAXq/NormalizeFasta.fasta does not exist. Please see for help creating it.

Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
20/05/28 10:00:10 INFO ShutdownHookManager: Shutdown hook called
20/05/28 10:00:10 INFO ShutdownHookManager: Deleting directory /tmp/spark-0ec24ec5-7519-42d9-a6f7-316529086161
Using GATK jar /usr/local/share/gatk4-
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /usr/local/share/gatk4- FindBadGenomicKmersSpark -R /ySLAXq/NormalizeFasta.fasta -O test.txt
INFO [job FindBadGenomicKmers.cwl] Max memory used: 252MiB
ERROR [job FindBadGenomicKmers.cwl] Job error:
("Error collecting output for parameter 'kmers_to_ignore':\nFindBadGenomicKmers.cwl:44:5: Did not find output file with glob pattern: '['test.txt']'", {})
WARNING [job FindBadGenomicKmers.cwl] completed permanentFail
WARNING Final process status is permanentFail

Although tool requirements are set to access directory containing reference genome fasta file and it’s dictionary file. Tool is unable to access reference genome dictionary file.