Nextflow Registry | nf-core/phispy@0.0.0-6c4ed3a

nf-core/phispy @ 0.0.0-6c4ed3a

Predict prophages in bacterial genomes

genomics virus phage prophage annotation identification

Latest version: 0.0.0-6c4ed3a

Total downloads: 10

Source: nf-core/modules

Authors: @jvfe

Maintainers: @jvfe

Predict prophages in bacterial genomes

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

include { PHISPY } from 'nf-core/phispy'

MIT License

Process

`Name`	`PHISPY`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`gbk` file	Genome file in .gbk or .gbff format. `*.{gbk,gbff}`

Output 12 channels

#1 gbk tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.gb*` file	A duplicate GenBank record that is the same as the input record, but we have inserted the prophage information, including att sites into the record. `*.{gbk,gbff}`

#2 log tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.log` file	File containing the PhiSpy execution log `*.{log}`

#3 versions

`versions.yml` file	File containing software versions `versions.yml`

#4 phage_gbk tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}_phage.gbk` file	Phage sequences extracted from the genome. `*.{gbk}`

#5 coordinates tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.tsv` file	Coordinates of each prophage identified in the genome, and their att sites (if found). `*.{tsv}`

#6 information tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}_prophage_information.tsv` file	File containing all the genes of the genome, one per line. The tenth column describes how likely the gene is a phage gene. `*.{tsv}`

#7 phage_fasta tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}_phage.fasta` file	Phage sequences extracted from the genome. `*.{fasta}`

#8 bacteria_gbk tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}_bacteria.gbk` file	Genome sequences identified as bacterial. `*.{gbk}`

#9 prophage_gff tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}_prophage.gff3` file	Prophage information in GFF3 format. `*.{gff3}`

#10 prophage_tbl tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}_prophage.tbl` file	File containing prophage number and its location in the genome. `*.{tbl}`

#11 prophage_tsv tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}_prophage.tsv` file	A file containing simpler version of the coordinates file, with only prophage number, contig, start and stop. `*.{tsv}`

#12 bacteria_fasta tuple

`meta` map