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Cromwell doesn't seem to be running Docker

Here is the error I'm getting:

2019-03-04 11:07:23,570 cromwell-system-akka.dispatchers.api-dispatcher-78 INFO  - Unspecified type (Unspecified version) workflow c737c64b-b611-4d04-80e6-a9c2f87587b1 submitted
2019-03-04 11:07:35,341 cromwell-system-akka.dispatchers.engine-dispatcher-6 INFO  - 1 new workflows fetched
2019-03-04 11:07:35,342 cromwell-system-akka.dispatchers.engine-dispatcher-6 INFO  - WorkflowManagerActor Starting workflow UUID(c737c64b-b611-4d04-80e6-a9c2f87587b1)
2019-03-04 11:07:35,343 cromwell-system-akka.dispatchers.engine-dispatcher-6 INFO  - WorkflowManagerActor Successfully started WorkflowActor-c737c64b-b611-4d04-80e6-a9c2f87587b1
2019-03-04 11:07:35,344 cromwell-system-akka.dispatchers.engine-dispatcher-6 INFO  - Retrieved 1 workflows from the WorkflowStoreActor
2019-03-04 11:07:35,375 cromwell-system-akka.dispatchers.engine-dispatcher-34 INFO  - MaterializeWorkflowDescriptorActor [UUID(c737c64b)]: Parsing workflow as WDL draft-2
2019-03-04 11:07:35,680 cromwell-system-akka.dispatchers.engine-dispatcher-34 INFO  - MaterializeWorkflowDescriptorActor [UUID(c737c64b)]: Call-to-Backend assignments: helloMethylationPipeline.MethylationPipeline -> Local
2019-03-04 11:07:36,842 cromwell-system-akka.dispatchers.engine-dispatcher-32 INFO  - WorkflowExecutionActor-c737c64b-b611-4d04-80e6-a9c2f87587b1 [UUID(c737c64b)]: Starting helloMethylationPipeline.MethylationPipeline
2019-03-04 11:07:37,446 cromwell-system-akka.dispatchers.backend-dispatcher-82 INFO  - BackgroundConfigAsyncJobExecutionActor [UUID(c737c64b)helloMethylationPipeline.MethylationPipeline:NA:1]: `ls > Sample1.txt
chmod 755 FastQC/fastqc
FastQC/fastqc /cromwell-executions/helloMethylationPipeline/c737c64b-b611-4d04-80e6-a9c2f87587b1/call-MethylationPipeline/inputs/-1184404984/SRR3997871_1.fastq`
2019-03-04 11:07:37,534 cromwell-system-akka.dispatchers.backend-dispatcher-82 INFO  - BackgroundConfigAsyncJobExecutionActor [UUID(c737c64b)helloMethylationPipeline.MethylationPipeline:NA:1]: executing: # make sure there is no preexisting Docker CID file
rm -f /home/len/Dropbox/Programming/MethylationPipeline/cromwell-executions/helloMethylationPipeline/c737c64b-b611-4d04-80e6-a9c2f87587b1/call-MethylationPipeline/execution/docker_cid
# run as in the original configuration without --rm flag (will remove later)
docker run \
  --cidfile /home/len/Dropbox/Programming/MethylationPipeline/cromwell-executions/helloMethylationPipeline/c737c64b-b611-4d04-80e6-a9c2f87587b1/call-MethylationPipeline/execution/docker_cid \
  -i \
   \
  --entrypoint /bin/bash \
  -v /home/len/Dropbox/Programming/MethylationPipeline/cromwell-executions/helloMethylationPipeline/c737c64b-b611-4d04-80e6-a9c2f87587b1/call-MethylationPipeline:/cromwell-executions/helloMethylationPipeline/c737c64b-b611-4d04-80e6-a9c2f87587b1/call-MethylationPipeline \
  gcr.io/docker-215501/[email protected]:ba8767c5a8d468886b0ca5cc14486cc217bea758da6effb49a520df801cf4bfb /cromwell-executions/helloMethylationPipeline/c737c64b-b611-4d04-80e6-a9c2f87587b1/call-MethylationPipeline/execution/script

# get the return code (working even if the container was detached)
rc=$(docker wait `cat /home/len/Dropbox/Programming/MethylationPipeline/cromwell-executions/helloMethylationPipeline/c737c64b-b611-4d04-80e6-a9c2f87587b1/call-MethylationPipeline/execution/docker_cid`)

# remove the container after waiting
docker rm `cat /home/len/Dropbox/Programming/MethylationPipeline/cromwell-executions/helloMethylationPipeline/c737c64b-b611-4d04-80e6-a9c2f87587b1/call-MethylationPipeline/execution/docker_cid`

# return exit code
exit $rc
2019-03-04 11:07:41,495 cromwell-system-akka.dispatchers.backend-dispatcher-81 INFO  - BackgroundConfigAsyncJobExecutionActor [UUID(c737c64b)helloMethylationPipeline.MethylationPipeline:NA:1]: job id: 11996
2019-03-04 11:07:41,502 cromwell-system-akka.dispatchers.backend-dispatcher-82 INFO  - BackgroundConfigAsyncJobExecutionActor [UUID(c737c64b)helloMethylationPipeline.MethylationPipeline:NA:1]: Status change from - to Done
2019-03-04 11:07:42,985 cromwell-system-akka.dispatchers.engine-dispatcher-9 ERROR - WorkflowManagerActor Workflow c737c64b-b611-4d04-80e6-a9c2f87587b1 failed (during ExecutingWorkflowState): Job helloMethylationPipeline.MethylationPipeline:NA:1 exited with return code 127 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/len/Dropbox/Programming/MethylationPipeline/cromwell-executions/helloMethylationPipeline/c737c64b-b611-4d04-80e6-a9c2f87587b1/call-MethylationPipeline/execution/stderr.
 chmod: cannot access ‘FastQC/fastqc’: No such file or directory
/cromwell-executions/helloMethylationPipeline/c737c64b-b611-4d04-80e6-a9c2f87587b1/call-MethylationPipeline/execution/script: line 24: FastQC/fastqc: No such file or directory

2019-03-04 11:07:42,994 cromwell-system-akka.dispatchers.engine-dispatcher-9 INFO  - WorkflowManagerActor WorkflowActor-c737c64b-b611-4d04-80e6-a9c2f87587b1 is in a terminal state: WorkflowFailedState

I tried attaching files but I'm getting a "file format not allowed" error. Here are my files:

MethylationPipeline.wdl

workflow helloMethylationPipeline {
  call MethylationPipeline
}

task MethylationPipeline {
  String sampleName
  String docker
  File inputFasta   
  command {
    ls > ${sampleName}.txt
    chmod 755 FastQC/fastqc
    FastQC/fastqc ${inputFasta}
  }
  output {
    File list ="${sampleName.txt}"
  }
  runtime {
        docker: docker
  }
}

MethylationPipeline.json

{
    "helloMethylationPipeline.MethylationPipeline.sampleName":"Sample1",
    "helloMethylationPipeline.MethylationPipeline.docker":"gcr.io/docker-215501/methylation-pipeline",
    "helloMethylationPipeline.MethylationPipeline.inputFasta":"/home/len/sratoolkit.2.9.2-ubuntu64/SRR3997871_1.fastq"
}

Dockerfile

FROM java:openjdk-8-jre

RUN wget "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.8.zip"
RUN unzip fastqc_v0.11.8.zip

I'm running Cromwell 36 on Linux Mint 19. I did the ls command and expected to get a list of files and directories in the Docker container, but it seems to list the files and directories in the executions directory.

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