Hello!
Hope you and yours are doing well. I am using multigather to query protein sequences against each other, and primarily use the csv file for downstream processing. As is, if the signatures in `--query query.sig` were created from one fasta file with e.g. `--singleton`, then all results iteratively overwrite each other into the same csv file. This proposed change adds the md5sum to the query file to ensure uniqueness. Other suggestions are welcome!

(not tested yet)

Warmest,
Olga

…o ctb_update_2065

…o ctb_update_2065

Note: PR into #2065.

This PR updates #2065 with all the changes from `latest`. This includes
the fix & update to multigather in
#2322, which:
- fixes the output of multigather to include more than one line 😆 
- prints out the output filename
- supports `--output-dir`

No functional changes are made beyond the merge, so some tests are still
failing; will discuss fixes in yet a new PR :).

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: Keya Barve <[email protected]>
Co-authored-by: ccbaumler <[email protected]>
Co-authored-by: Tessa Pierce Ward <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Taylor Reiter <[email protected]>
Co-authored-by: Erik Young <[email protected]>
Co-authored-by: David Koslicki <[email protected]>
Co-authored-by: Luiz Irber <[email protected]>
Co-authored-by: Colton Baumler <[email protected]>
Co-authored-by: Luiz Irber <[email protected]>
Co-authored-by: N. Tessa Pierce-Ward <[email protected]>
Co-authored-by: Peter Cock <[email protected]>
Co-authored-by: Francesco Beghini <[email protected]>
Co-authored-by: Jason Stajich <[email protected]>
Co-authored-by: Katrin Leinweber <[email protected]>

…o olgabot-patch-2

…rmash into fix_multigather_output

…o fix_multigather_output

…o fix_multigather_output_merge

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