try porting mmseqs/search to nf-test

[famosab]

PR checklist

Closes #XXX
Related to #7211

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the module conventions in the contribution docs
• If necessary, include test data in your PR.
• Remove all TODO statements.
• Emit the versions.yml file.
• Follow the naming conventions.
• Follow the parameters requirements.
• Follow the input/output options guidelines.
• Add a resource label
• Use BioConda and BioContainers if possible to fulfil software requirements.
• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
  • For modules:
    • nf-core modules test <MODULE> --profile docker
    • nf-core modules test <MODULE> --profile singularity
    • nf-core modules test <MODULE> --profile conda
  • For subworkflows:
    • nf-core subworkflows test <SUBWORKFLOW> --profile docker
    • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
    • nf-core subworkflows test <SUBWORKFLOW> --profile conda

I tried porting but I always run into the following error:

│                                                                                                                                                                                                                                                                                                                                                                        │
│   Assertion failed:                                                                                                                                                                                                                                                                                                                                                    │
│                                                                                                                                                                                                                                                                                                                                                                        │
│   2 of 2 assertions failed                                                                                                                                                                                                                                                                                                                                             │
│                                                                                                                                                                                                                                                                                                                                                                        │
│   Nextflow stdout:                                                                                                                                                                                                                                                                                                                                                     │
│                                                                                                                                                                                                                                                                                                                                                                        │
│   ERROR ~ Script compilation error                                                                                                                                                                                                                                                                                                                                     │
│   - file : /Users/famke/02-nf-core/modules/.nf-test-1f5468570864d0273649d793a99b787b.nf                                                                                                                                                                                                                                                                                │
│   - cause: The LHS of an assignment should be a variable or a field accessing expression @ line 56, column 22.                                                                                                                                                                                                                                                         │
│                      input[0] = MMSEQS_CREATEDB_QUERY.out.db,                                                                                                                                                                                                                                                                                                          │
│                           ^                                                                                                                                                                                                                                                                                                                                            │
│                                                                                                                                                                                                                                                                                                                                                                        │
│   1 error                                                                                                                                                                                                                                                                                                                                                              │
│                                                                                                                                                                                                                                                                                                                                                                        │
│                                                                                                                                                                                                                                                                                                                                                                        │
│    -- Check '/Users/famke/02-nf-core/modules/.nf-test/tests/1f5468570864d0273649d793a99b787b/meta/nextflow.log' file for details                                                                                                                                                                                                                                       │
│   Nextflow stderr:  

[prototaxites]

Hopefully this will make the tests run!

[famosab]

Now I still get:

│   Test [1f546857] 'sarscov2 - test-search' FAILED (6.297s)                                                                                                                                                                                                   │
│                                                                                                                                                                                                                                                              │
│   Assertion failed:                                                                                                                                                                                                                                          │
│                                                                                                                                                                                                                                                              │
│   2 of 2 assertions failed                                                                                                                                                                                                                                   │
│                                                                                                                                                                                                                                                              │
│   Nextflow stdout:                                                                                                                                                                                                                                           │
│                                                                                                                                                                                                                                                              │
│   ERROR ~ Error executing process > 'MMSEQS_CREATEDB_QUERY (test_query)'                                                                                                                                                                                     │
│                                                                                                                                                                                                                                                              │
│   Caused by:                                                                                                                                                                                                                                                 │
│     Process `MMSEQS_CREATEDB_QUERY (test_query)` terminated with an error exit status (132)                                                                                                                                                                  │
│                                                                                                                                                                                                                                                              │
│                                                                                                                                                                                                                                                              │
│   Command executed:                                                                                                                                                                                                                                          │
│                                                                                                                                                                                                                                                              │
│     if [ "false" == "true" ]; then                                                                                                                                                                                                                           │
│         gzip -c -d contigs.fasta > contigs.fasta                                                                                                                                                                                                             │
│     fi                                                                                                                                                                                                                                                       │
│                                                                                                                                                                                                                                                              │
│     mkdir -p test_query                                                                                                                                                                                                                                      │
│                                                                                                                                                                                                                                                              │
│     mmseqs \                                                                                                                                                                                                                                                 │
│         createdb \                                                                                                                                                                                                                                           │
│         contigs.fasta \                                                                                                                                                                                                                                      │
│         test_query/test_query \                                                                                                                                                                                                                              │
│          \                                                                                                                                                                                                                                                   │
│         --compressed 1                                                                                                                                                                                                                                       │
│                                                                                                                                                                                                                                                              │
│     cat <<-END_VERSIONS > versions.yml                                                                                                                                                                                                                       │
│     "MMSEQS_CREATEDB_QUERY":                                                                                                                                                                                                                                 │
│         mmseqs: $(mmseqs | grep 'Version' | sed 's/MMseqs2 Version: //')                                                                                                                                                                                     │
│     END_VERSIONS                                                                                                                                                                                                                                             │
│                                                                                                                                                                                                                                                              │
│   Command exit status:                                                                                                                                                                                                                                       │
│     132                                                                                                                                                                                                                                                      │
│                                                                                                                                                                                                                                                              │
│   Command output:                                                                                                                                                                                                                                            │
│     (empty)                                                                                                                                                                                                                                                  │
│                                                                                                                                                                                                                                                              │
│   Command error:                                                                                                                                                                                                                                             │
│     .command.sh: line 13:    35 Illegal instruction     mmseqs createdb contigs.fasta test_query/test_query --compressed 1                                                                                                                                   │
│                                                                                                                                                                                                                                                              │
│   Work dir:                                                                                                                                                                                                                                                  │
│     /Users/famke/02-nf-core/modules/.nf-test/tests/1f5468570864d0273649d793a99b787b/work/cc/491340106cd3202f039939bdafd8fa                                                                                                                                   │
│                                                                                                                                                                                                                                                              │
│   Container:                                                                                                                                                                                                                                                 │
│     quay.io/biocontainers/mmseqs2:16.747c6--pl5321h6a68c12_0                                                                                                                                                                                                 │
│                                                                                                                                                                                                                                                              │
│   Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`                                                                                                                            │
│                                                                                                                                                                                                                                                              │
│    -- Check '/Users/famke/02-nf-core/modules/.nf-test/tests/1f5468570864d0273649d793a99b787b/meta/nextflow.log' file for details                                                                                                                             │
│   Nextflow stderr:            

[jfy133]

@famosab I think I will take some of your initial work here into the removing teh compress module PR from Jasmin, as I guess the snapshot might change due to the removal of teh compression

[famosab]

Just close it if its obsolete :)

[SPPearce]

I was finishing this off here before James started so I finished it off (letting him know).
This PR should be good to merge if the checks pass, I included removing the compression.

Stale

[jfy133]

I don't see anything problematic, maybe just a comment why just checking for file names

[jfy133]

@SPPearce I'm going to force merge this as your tests are passing but easysearch is fixed in the other PR