Nextflow Registry | nf-core/genomad/endtoend@0.0.0-6c4ed3a

nf-core/genomad/endtoend @ 0.0.0-6c4ed3a

Identify mobile genetic elements present in genomic assemblies

metagenomics genomad database download phage virus plasmid

Latest version: 0.0.0-6c4ed3a

Total downloads: 13

Source: nf-core/modules

Authors: @CarsonJM

Maintainers: @CarsonJM @gallvp

Identify mobile genetic elements present in genomic assemblies

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

include { GENOMAD_ENDTOEND } from 'nf-core/genomad/endtoend'

MIT License

Process

`Name`	`GENOMAD_ENDTOEND`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`fasta` file	FASTA file containing contigs/scaffolds/chromosomes `*.{fasta,fna,fa}`

`genomad_db` directory	Directory pointing to geNomad database

Output 15 channels

#1 provirus tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`_find_proviruses/_provirus.tsv` file	Detailed output of each provirus identified by geNomad's find_proviruses module `*_provirus.tsv`

#2 taxonomy tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`_annotate/_taxonomy.tsv` file	Detailed output of geNomad's marker gene taxonomy analysis `*_taxonomy.tsv`

#3 virus_fasta tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`_summary/_virus.fna.gz` file	FASTA file containing predicted virus sequences `*_virus.fna`

#4 virus_genes tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`_summary/_virus_genes.tsv` file	TSV file containing predicted virus genes and their annotations `*_virus_genes.tsv`

#5 compositions tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`_score_calibration/_compositions.tsv` file	OPTIONAL - Predicted sample composition when `--enable-score-calibration` is used `*_compositions.tsv`

#6 plasmid_fasta tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`_summary/_plasmid.fna.gz` file	FASTA file containing predicted plasmid sequences `*_plasmid.fna`

#7 plasmid_genes tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`_summary/_plasmid_genes.tsv` file	TSV file containing predicted plasmid genes and their annotations `*_plasmid_genes.tsv`

#8 virus_summary tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`_summary/_virus_summary.tsv` file	TSV file containing a summary of geNomad's virus predictions `*_virus_summary.tsv`

#9 virus_proteins tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`_summary/_virus_proteins.faa.gz` file	FASTA file containing predicted virus protein sequences `*_virus_proteins.faa`

#10 plasmid_summary tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`_summary/_plasmid_summary.tsv` file	TSV file containing a summary of geNomad's plasmid predictions `*_plasmid_summary.tsv`

#11 plasmid_proteins tuple