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Add a dry-run option #58

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magicDGS opened this issue Feb 21, 2018 · 2 comments
Open

Add a dry-run option #58

magicDGS opened this issue Feb 21, 2018 · 2 comments

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@magicDGS
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Currently, the --verbose option prints the parsed inputs in the terminal and then exit; nevertheless, there is no real check for the arguments or requirements (such as ReadTools version or existance of files).

It will be nice to debug the current behaviour to have a --dry-run option that will construct the pipeline internally and do the checks, printing on the command line what the pipeline will be (this can be a good addition also if not dry-run is specified, at the beginning of the output). For example, it could say:

PIPELINE (job = ${job_description})
===================================
* Indexing (${reference})
* Upload (${inputs})
* Trimming (${trimming_script} with arguments: "${trim_args}")
* Map (${mapper} with arguments  "${mapper_args}")

WARNING: trimming is perform on upload and it is OBSOLETE

This will be useful for debugging, but also for the final user to check how the procedure will be.

@robmaz
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robmaz commented Feb 21, 2018

Good idea in principle, but difficult to implement with the current convoluted structure.

@magicDGS magicDGS added this to the Long term changes milestone Feb 21, 2018
@magicDGS
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So for the long term!

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