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Implement a "blr init" command #94

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marcelm opened this issue Sep 16, 2019 · 0 comments
Closed

Implement a "blr init" command #94

marcelm opened this issue Sep 16, 2019 · 0 comments

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@marcelm
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marcelm commented Sep 16, 2019

While #92 deals with blr run, we should also have a blr init command that initializes an analysis directory.

Considerations:

  • Splitting up initialization and running in this way makes sense because we want to give the user the opportunity to configure the pipeline before running it. The init command can create a nicely commented template configuration in which it should be mostly self-explanatory what the settings do. This is easier to use than requiring the user to provide a configuration file from scratch.

  • BLR will have different types of pipelines (e.g., whole-genome haplotyping, metagenomic analysis). How does the user choose which pipeline to run? We can have either different commands (blr wgh and blr meta) or options (blr init --wgh, blr init --meta).

marcelm added a commit that referenced this issue Sep 25, 2019
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marcelm added a commit that referenced this issue Sep 27, 2019
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