catpack_contigs

Description¶

Taxonomic classification of long DNA sequences and metagenome assembled genomes (e.g. contigs, MAGs / bins).

This module is used by the following pipelines:

nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install catpack/contigs

CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)

Name	Type	Description	Pattern
`meta`	map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`	-
`contigs`	file	A nucleotide FASTA file containing long DNA sequences such as contigs.	`*.{fasta,fna,fa,fas}`
`meta2`	map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`	-
`database`	directory	Directory containing CAT_pack database files (e.g. output from CAT_pack prepare)	`*/`
`meta3`	map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`	-
`taxonomy`	directory	Directory containing CAT_pack taxonomy files (e.g. output from CAT_pack prepare)	`*/`
`meta4`	map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`	-
`proteins`	directory	Optional pre predicted-made proteins FASTA	`*.{fasta,faa,fa,fas}`
`meta5`	map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`	-
`diamond_table`	directory	Optional pre-made DIAMOND alignment table	`*`

Name	Type	Pattern
`orf2lca`	file	-
`contig2classification`	file	-
`log`	file	-
`diamond`	file	-
`faa`	file	-
`gff`	file	-
`versions`	file	-