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elixir-no-nels / rbFlow-Germline

A workflow engine with a germline calling pipeline running in a container
MIT License
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Define behavior and need for -p and -v options for rubyFlowLite cluster pipeline #2

Open oskarvid opened 6 years ago

oskarvid commented 6 years ago

The desired behavior is the option to choose to run either or both of the preprocessing or variant calling parts of the pipeline. Currently the implementation executes both parts as one pipeline. This will not be part of the first milestone since the focus for the first milestone is to deliver a functioning pipeline that accomplishes the basic task of analyzing input files correctly. The next milestone will include enhancements that are not essential for basic execution.

oskarvid commented 5 years ago

@GhisF You added this feature but didn't update this issue when you did, please do. I tried to test it but it throws this error when I use -p: wf_elixir_GermlineCaller_csv_singularity.rb:161:in <main>': undefined local variable or method preprocessing' for main:Object (NameError) Do you get the same error if you clone this repository and use -p?

GhisF commented 5 years ago

Should be options[:preprocessing] and not preprocessing

The error should be fixed now

oskarvid commented 5 years ago

To do: Test on TSD.