Nextflow Registry | nf-core/catpack/contigs@0.0.0-6c4ed3a

nf-core/catpack/contigs @ 0.0.0-6c4ed3a

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

Latest version: 0.0.0-6c4ed3a

Total downloads: 11

Source: nf-core/modules

Authors: @jfy133

Maintainers: @jfy133

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

Add the following snippet to your workflow script to include this module.

include { CATPACK_CONTIGS } from 'nf-core/catpack/contigs'

MIT License

Process

`Name`	`CATPACK_CONTIGS`

Input 5 channels

#1 tuple

`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}`

#2 tuple

`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) `*/`

#3 tuple

`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) `*/`

#4 tuple

`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}`

#5 tuple

`meta5` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`diamond_table` directory	Optional pre-made DIAMOND alignment table `*`

Output 7 channels

#1 faa tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.predicted_proteins.faa` file	FAA file of DIAMOND predicted proteins hits

#2 gff tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.gff` file	GFF file of DIAMOND predicted proteins hits

#3 log tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.log` file	Log file with run messages and basic statistics

#4 diamond tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.diamond` file	Intermediate DIAMOND TSV summary output file with alignment results

#5 orf2lca tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.ORF2LCA.txt` file	A TSV file with per-ORF hit stats and identified lineage `*.ORF2LCA.txt`

#6 versions_catpack tuple

`${task.process}` string	The process the versions were collected from
`catpack` string	The tool name
`CAT_pack --version \| sed 's/CAT_pack pack v//g;s/ .*//g'` eval	The expression to obtain the version of the tool

#7 contig2classification tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.contig2classification.txt` file