Using dash in docker parameter results in error

[ddemaeyer]

Adding paths to the platform volume mounting for docker with dashes results in invalid definitions for docker:

I.e.

- name: output-dir
  mount: /output

Running example 
./output/scrublet --input /data/pbmc_1k_protein_v3_filtered_feature_bc_matrix.h5ad --data $(pwd)/test --output-dir $(dirname $(dirname $(pwd)))/test-output --output /output/pbmc_1k_protein_v3_filtered_feature_bc_matrix.scrublet.h5ad

Results in 
./output/scrublet: line 54: VOLUME_OUTPUT-DIR=/projects/processedData/2020/CS/ddemaey1/git/scPipelineViash/test-output: No such file or directory
docker: Error response from daemon: create -DIR: "-DIR" includes invalid characters for a local volume name, only "[a-zA-Z0-9][a-zA-Z0-9_.-]" are allowed. If you intended to pass a host directory, use absolute path.
See 'docker run --help'.
[ddemaey1@awsaivirl1108 scrublet]$ ./run_test.sh 

This can be resolved by renaming

- name: outputdir
  mount: /output

[rcannood]

Hmm. I think allowing names with dashes will cause all sorts of downstream problems in bash. I suggest using outputdir, output_dir, or outputDir instead.

I added an extra check to the class of the docker volumes, so that a more useful error will be produced during the viash export instead of when you try to run the code.

Is this okay for you?

[ddemaeyer]

Yes

Op wo 6 mei 2020 11:08 schreef Robrecht Cannoodt notifications@github.com:

Hmm. I think allowing names with dashes will cause all sorts of downstream problems in bash. I suggest using outputdir, output_dir, or outputDir instead.

I added an extra check to the class of the docker volumes, so that a more useful error will be produced during the viash export instead of when you try to run the code.

Is this okay for you?

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