Remove compressed flag from all mmseqs modules

[jasmezz]

We've been struggling a long time with mmseqs modules which wouldn't run with the GTDB database (in the nf-core/funcscan pipeline in our case). The reproducible error occurred always late in the "prefilter" step of the mmseqs runs with infos like aggregatetaxweights died.

@Darcy220606 recently solved the mystery:

[The flag] --compressed 1 is hardcoded across all mmseqs module on nf-core, that apparently is creating a problem when no contigs pass the prefilter step at a certain kmer size, which is a bit downstream in the general prefilter process (esp. that we have a relatively strict parameters). This confuses the tool as the files are 'emptily compressd'.

Hence, we ran all modules with the --compressed 1 removed and now they run through successfully even with the big GTDB database.
Taking this as confirmation, the flag is removed in all mmseqs modules in this PR. The flag can then be re-added as a parameter on pipeline level if needed.

PR checklist

Closes #XXX

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[famosab]

Seems like some of the snapshots need to be updated for the tests to pass :)

[SPPearce]

Ugh, 3 of these modules are still in pytest. Are you able to port them to nf-test?

[famosab]

• mmseqs/search
• mmseqs/easysearch

and?

[SPPearce]

• mmseqs/search
• mmseqs/easysearch

and?

• tsv2exprofiledb

[famosab]

I tried with 2/3 modules and ran into a couple of problems but maybe that can be a starting point for the porting :)

[jfy133]

I will work on the nf-test conversion of the three outstanding modules

[jfy133]

OK @SPPearce is finishing mmseqs search

[jfy133]

I've just started mmseqs easyesearch ✅

[jfy133]

@sateeshperi when I run the tests locally for the failed ones, they pass fine.

Where did you work on tsv2exprofiledb? Gitpod?

[sateeshperi]

yes

[sateeshperi]

note for future:

process MMSEQS_CONTIG_TAXONOMY:MMSEQS_DATABASES (Kalamari) did experience failure to download the db

  >   01/16 06:53:52 [NOTICE] Download complete: tmp//7555276924772959017/taxonomy/taxdump.tar.gz.aria2
    >   
    >   Download Results:
    >   gid   |stat|avg speed  |path/URI
    >   ======+====+===========+=======================================================
    >   e96c36|OK  |    48MiB/s|tmp//7555276924772959017/taxonomy/taxdump.tar.gz.aria2
    >   
    >   Status Legend:
    >   (OK):download completed.
    >   double free or corruption (out)
    >   Aborted (core dumped)
    >   Error: createbintaxonomy failed
    >   Error: createtaxdb died
    ```

[jfy133]

Which is related to an internal problem with mmseqs, something we can't work around