s3 support for toil-cwl-runner?

The quickstart guide states:

When running a CWL workflow on AWS, input files can be provided either on the local file system or in S3 buckets using s3:// URI references. Final output files will be copied to the local file system of the leader node."

However, I consistently get the error at this point in the code: "file." % (knownfile, self.pathmapper.mapper(knownfile)[0])) reporting: WorkflowException: Input file https://s3.amazonaws.com/<bucket>/<file> (at //s3.amazonaws.com/<bucket>/<file>) not found or is not a regular file.

or, if I use the s3:// URI system I get: WorkflowException: Input file s3://<bucket>/<file> (at //<bucket>/<file>) not found or is not a regular file.

where <bucket> and <file> are obviously filled in with my specific bucket and file.

┆Issue is synchronized with this JIRA Story ┆Issue Number: TOIL-103

[BJWiley233]

Yes here are my steps. Thanks!

aws ec2 import-key-pair --key-name "my-key2" --public-key-material fileb://~/.ssh/id_rsa.pub

toil launch-cluster test-cluster --zone us-west-2a --leaderNodeType t2.large --keyPairName my-key2

toil rsync-cluster --zone us-west-2a test-cluster _bcftools_norm.cwl _norm.yml :/tmp

toil ssh-cluster --zone us-west-2a test-cluster 

mkdir ~/.aws
## to add in my Access ID and Key
vim ~/.aws/credentials

toil-cwl-runner /tmp/_bcftools_norm.cwl /tmp/_norm.yml 

toil destroy-cluster test-cluster

forgot to add my input yaml:

---
reference: 
  class: File
  path: s3://test-*******-bucket/GRCh38_full_analysis_set_plus_decoy_hla.fa
vcf: 
  class: File
  path: s3://test-*******-bucket/mutect_full.first.vcf.gz
output_vcf_name: "test.bcftools.norm.vcf.gz"

[BJWiley233]

Also is there a command that will terminate the instances after I run toil destroy-cluster? This didn’t shut down the instances and I was still billed. Do we manually need to terminate the instances through the aws cli or AWS console?