Add BAQLaVa to pipeline

[seandavi]

From slack:

The short-term goal is that it would be nice to include BAQLaVa there

Either a PR, or if it is easier, supply:

1. Any software installation including version
2. The exact command line with recommended flags and options
3. The expected output files (specific names if possible)

And we can iterate on getting the code into the pipeline.

[sagun98]

Hi @seandavi ,
Thank you for starting this thread. I am more than happy to iterate with you for getting the BAQLaVa into the curatedMetagenomicsNextflow pipeline + getting recommendation on best practices for NF workflows for our own pipelines. Please let me know if you run into any issues for the following the installation and the run.

1. Any software installation including version:
   BAQLaVa User Manual Link: https://github.com/biobakery/baqlava?tab=readme-ov-file#step-1-option-2-install-using-pypi

baqlava v0.5 (https://pypi.org/project/baqlava/)
baqlava database: baqlava_database --download database baqlava-db /path/to/install_database
HUMAnN=3.9 (https://github.com/biobakery/humann)
AnADAMA2>=0.10.0 (https://github.com/biobakery/anadama2)
Python>=3.10 (https://github.com/biobakery/anadama2)

2. The exact command line with recommended flags and options

baqlava -i baqlava/examples/baqlava_demo.fq -o <PATH/TO/OUTPUT> --nucdb examples/BAQLaVa.V0.5.nucleotide/ --protdb examples/BAQLaVa.V0.5.protein/ --bypass-bacterial-depletion

3. The expected output files:

<FILENAME>_BAQLaVa_profile.txt
<FILENAME>_bacterial_depleted.fa
<FILENAME>_tempfile_markers.txt
<FILENAME>_tempfile_proteins.txt