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bioforensics / yeat

YEAT: Your Everyday Assembly Tool
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Accepting uncompressed fastq files #31

Closed danejo3 closed 1 year ago

danejo3 commented 1 year ago

The purpose of this PR is to resolve #26 .

To run YEAT, the user is required to provide two compressed fastq files (ie., .gz).

Instead of forcing compressed input files, this PR aims to allow the flexibility of users to pass in both compressed and/or uncompressed reads.

To do this, a snakemake rule, copyinput, was updated.

If users passed in an uncompressed file(s), YEAT will automatically compress it after the file has been copied over into the seq/input directory.

This early compression will prevent fastp from crashing because of the incompatible extensions assigned to the uncompressed file was passed in through the CLI.

danejo3 commented 1 year ago

Adding @lovettse to this PR as well.

danejo3 commented 1 year ago

Hold on; I messed my code up. Sorry.

danejo3 commented 1 year ago

Okay! Ready! Sorry!