[DOCKTESTERS] Issues with Consensus Docker

[Miguel Vazquez]

Hi all,

I've started trying to test the Consensus Docker and I've ran into a few
difficulties. Some pertain the application itself and some I are questions
I have related to CWL or Docker.

1- Missing input dbs_dir: The documentation suggests that this is a
directory with resources that need to be set up beforehand using the same
docker container with different parameters. I'm not sure how to handle
this. To keep going I've just pointed to some arbitrary directory

2- Missing tbi files on input VCFs: The CWL explicitly asks for the input
VCF. In the documentation it seems like the inputs are in fact compressed
with gzip. Up to here is fine, though I wonder if there would not be a more
explicit way to indicate this in. The problem comes when I run it that I
get an error complaining about a missing tbi file:

  Missing input file [Errno 2] No such file or directory:
'/mnt/1TB/work/DockerTest-Miguel/data/DO52621//broad.oxoG.annotated.vcf.gz
*.tbi*'

It is not a problem to produce it using tabix but what is confusing to me
is that there is no mention of any tbi file in the Dockstore.json file. How
does this work?

3- After producing the tbi files I get this error, which I think is related
to (1)

  Invalid filename: '' contains illegal characters


Best regards

Miguel

----Dockstore.json-----


{
  "broad_input_file": {
    "path": "/tmp/fill_me_in.txt",
    "class": "File"
  },
  "dkfz_embl_input_file": {
    "path": "/tmp/fill_me_in.txt",
    "class": "File"
  },
  "variant_type": "fill me in",
  "consensus_vcf_index": {
    "path": "/tmp/fill_me_in.txt",
    "class": "File"
  },



*  "dbs_dir": {    "path": "/tmp/fill_directory_in",    "class":
"Directory"  },*
  "muse_input_file": {
    "path": "/tmp/fill_me_in.txt",
    "class": "File"
  },
  "consensus_zipped_vcf": {
    "path": "/tmp/fill_me_in.txt",
    "class": "File"
  },
  "sanger_input_file": {
    "path": "/tmp/fill_me_in.txt",
    "class": "File"
  }
}
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