uclahs-cds / package-PipeVal

An easy to use CLI tool that can be used to validate different parameters in your NF script/pipeline.
GNU General Public License v2.0
5 stars 1 forks source link

Make input type optional #52

Closed aybeshlikyan closed 2 years ago

aybeshlikyan commented 2 years ago

Checklist

Formatting

File Updates

Docker Hub Auto Build Rules

Docker Image Testing

Test the Docker image with at least one sample. Verify the new Docker image works using:

docker run -u $(id -u):$(id -g) –w <working-directory> -v <directory-you-want-to-mount>:<how-you-want-to-mount-it-within-the-docker> --rm <docker-image-name> <command-to-the-docker-with-all-parameters>

My command:

docker build -t test-pipeval . -f docker/Dockerfile docker run -it --rm -v /Users/abeshlikyan/Infrastructure/public-tool-PipeVal/tests:/tool/tests test-pipeval pytest: All existing tests pass. Manual testing from the command line on sample files passed as well.

Description

Closes #51. Makes -t optional and sets default to file-input.

jarbet commented 2 years ago

Looks good to me! @jarbet I think this update should resolve the issue we touched on?

I think so.

@aybeshlikyan: Will this PR now allow run_validate_PipeVal to handle a channel input of cardinality 1? For example, only sending run_validate_PipeVal a channel/vector of file paths? If so, then I think this will solve the issues I'm having here.

In the past, @aybeshlikyan and @yashpatel6 sent run_validate_PipeVal an input channel of cardinality 2: mode (file type) and file_to_validate (file path). Will this PR still support your previous calls to run_validate_PipeVal, or will that code need to be updated?