subworkflows/mmseqs_contig_taxonomy
Assign taxonomy to contigs using the MMseqs2 workflow.
Input
Channel containing each fasta in nucleotide format as a distinct element with meta.
Structure: [ val(meta), path(fasta) ]
*.{fasta,fa,fna} Channel containing a database created by mmseqs2 databases.
Structure: [ path(mmseqsdb) ]
*/mmseqs/database Channel containing the ID of a database made available by developers of mmseqs2. Please refer to https://github.com/soedinglab/MMseqs2/wiki#downloading-databases for possible IDs to use.
Structure: [ val(id) ]
Output
Channel containing the tab seperated file with all assigned taxonomy.
Structure: [ val(meta), path(tsv) ]
*.tsv Channel containing the mmseqs database directory. Useful for when the databases is downloaded in the pipeline.
Structure: [ path(outputdir) ]
*/mmseqs_database Channel containing the database containing the taxonomic classification for each input fasta file.
Structure: [ path(outputdir) ]
*/sample_taxonomy Channel containing the database containing the mmseqs format of each input fasta file.
Structure: [ path(outputdir) ]
*/sample_db included modules and subworkflows
maintainer
