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bioforensics / yeat

YEAT: Your Everyday Assembly Tool
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Implementing MEGAHIT Into YEAT #13

Closed danejo3 closed 2 years ago

danejo3 commented 2 years ago

The purpose of this PR is to close #10 .

In order to run YEAT, users will be required to provide the type of assembler that the user would like to run.

For example,

yeat --assembly spades [read1] [read2]

In addition to the support for MEGAHIT, if the user would like to run multiple assemblers with the same reads, users can put a comma (",") after each assembler name.

For example,

yeat --assembly spades,megahit [read1] [read2]

As of right now, YEAT can only assembler read with spades and megahit. More assemblers will be added in the future.

danejo3 commented 2 years ago

PR is ready for review! @standage

danejo3 commented 2 years ago

Really? If you were to run yeat --assembly spades,megahit right now on a machine with 64 threads wouldn't Snakemake run them in parallel?

You are completely right! I didn't understand how Snakemake parallelizes multiple jobs until I just ran it.

danejo3 commented 2 years ago

Code is ready to be reviewed and merged!