Metaphlan

[tasapl]

Added functionality for selecting either kraken2 or metaphlan classifier. Added taxpasta module to standardize output regardless of classifier choice. Added new parameter "--classifier" allowing user to specify either kraken2 or metaphlan.

In order to run successfully:

• Download taxdump.tar.gz from https://ftp.ncbi.nih.gov/pub/taxonomy/
• Decompress and add the names.dmp and nodes.dmp files into the taxdump directory
• Change the directory of the variable "taxdump_dir" in line 382 of taxtriage.nf
• Download and decompress desired metaphlan database index (TOY used during testing due to file size limitations) from http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/
• Download and decompress the corresponding database bowtie index from http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/bowtie2_indexes/
• Change the metaphlan_db variable in line 381 to the path of the directory containing db files
• In main.nf for metaphlan nf-core file, edit the BT2_DB variable (line 33) and set "--index" flag in line 42 as the name of the db file