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ncbi / sra-human-scrubber

An SRA tool that takes as input local fastq file from a clinical infection sample, identifies and removes any significant human read, and outputs the edited (cleaned) fastq file that can safely be used for SRA submission.
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Srab 44 - k florek changes #16

Closed multikengineer closed 3 years ago

multikengineer commented 3 years ago

This includes all of k-florek's changes in a backwards compatible manner, and a tweak here and there.

rpetit3 commented 3 years ago

Looks good to me!

Not trying to be difficult here. but I think it's worth mentioning that by creating a new PR, @k-florek's contributions will not show up in the commits (https://github.com/ncbi/sra-human-scrubber/commits/master) or the contributors list (https://github.com/ncbi/sra-human-scrubber/graphs/contributors)

I think @k-florek's body of work is impressive and speaks for itself. But as an early career scientist, I've found GitHub commits to be an extremely valuable metric for documenting scientific contributions. You never know, you might one day get a PR that is the product of someone's entire internship!

multikengineer commented 3 years ago

@rpetit3 Not being difficult at all, and I fully agree. Since I could not take the changes as they were, and I was starting from the fork, I took the easier path. Had I been able to use the changes out of the box then I would have.

rpetit3 commented 3 years ago

Thank you very much Ken! It really means a lot. Cheers

rpetit3 commented 3 years ago

One alternative to consider is editing the files in https://github.com/ncbi/sra-human-scrubber/pull/15 to include the changes you added.

multikengineer commented 3 years ago

Before coffee rescued commits for PR #16 for this, closing to merge with history intact.