Revive sylph module, download 3 DBs

[ppreshant]

There's nf-core modules! please use them

Plan

• 1. PK makes a sylph folder ; with all these modules: sylph_profile
• 2. PK : Find our sylph DB path (found GTDB bacterial only) and make a nextflow.config variable for it

sylph_prok_db_file = "${params.db_base_dir}/gtdb-r220-c200-dbv1.syldb" // placeholder ; will use a dir/ instead of file when auto-downloading

• need: GTDB-bacterial, viral and eukaryotic. Refer to sylph-docs
• 3. Make the logic for if() conditioned run of sylph in the taxonomic_profiling subworkflow. Finish till here by Tues?
• 4. Austin: could test the sylph module within the subworkflow and move to the viral and eukaryotic issues

Status

• PK pulled the nf-core module and added a bacterial DB from the shared dir in the sylph_i73 branch
• @microbemarsh can start testing the module itself with a dummy entry workflow using test data from either : assets/examples/other_tools_files/sylph/ or assets/examples/data/small_metagenome in the same branch
• .. Keep updating here!

Record any small bugs/handy observations in the next thread please

[ppreshant]

Notes

record any bugs / thoughts / handy observations from making this stuff here