modules/gapseq_doall

Complete gapseq workflow from genome to gap-filled model

metabolic modelgap fillingpathway predictionbacteriagenome-scale modelcomplete workflow

https://github.com/nf-core/modules/[...]/modules/nf-core/gapseq/doall

Description

Complete gapseq workflow from genome to gap-filled model

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`fasta`
`:file`

Protein or genomic FASTA file

*.{fasta,fa,faa,fna,gz}

`medium`
`:file`

Optional medium definition file (CSV format)

*.csv

Output

name:type

description

pattern

`model`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*.RDS`
`:file`

Gap-filled metabolic model in RDS format

*.RDS

`tbl`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*.tbl`
`:file`

TBL files containing pathway and transporter predictions

*.tbl

`fna`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*.fna`
`:file`

Optional extracted sequences in FASTA format

*.fna

`log`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*.log`
`:file`

Log files from gapseq doall

*.log

`versions_gapseq`

`${task.process}`
`:string`

The name of the process

`gapseq`
`:string`

The name of the tool

`gapseq -v 2>&1 | grep -oP "\d+\.\d+\.\d+"`
`:string`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`gapseq`
`:string`

The name of the tool

`gapseq -v 2>&1 | grep -oP "\d+\.\d+\.\d+"`
`:string`

The expression to obtain the version of the tool

Tools

gapseq
AGPL-3.0-only

gapseq is designed to combine metabolic pathway analysis with metabolic network reconstruction and curation. The doall command runs the complete workflow: pathway prediction, transporter inference, model construction, and gap filling.

github.com/jotech/gapseq gapseq.readthedocs.io https://github.com/jotech/gapseq 10.1186/s13059-021-02295-1

modules/gapseq_doall

Description

Input

`meta`
`:map`

`fasta`
`:file`

`medium`
`:file`

Output

`model`

`meta`
`:map`

`*.RDS`
`:file`

`tbl`

`meta`
`:map`

`*.tbl`
`:file`

`fna`

`meta`
`:map`

`*.fna`
`:file`

`log`

`meta`
`:map`

`*.log`
`:file`

`versions_gapseq`

`${task.process}`
`:string`

`gapseq`
`:string`

`gapseq -v 2>&1 | grep -oP "\d+\.\d+\.\d+"`
`:string`

Topics

`versions`

`${task.process}`
`:string`

`gapseq`
`:string`

`gapseq -v 2>&1 | grep -oP "\d+\.\d+\.\d+"`
`:string`

Tools

gapseq
AGPL-3.0-only

included in

maintainer

get in touch

modules/gapseq_doall

Description

Input

meta:map

fasta:file

medium:file

Output

model

meta:map

*.RDS:file

tbl

meta:map

*.tbl:file

fna

meta:map

*.fna:file

log

meta:map

*.log:file

versions_gapseq

${task.process}:string

gapseq:string

gapseq -v 2>&1 | grep -oP "\d+\.\d+\.\d+":string

Topics

versions

${task.process}:string

gapseq:string

gapseq -v 2>&1 | grep -oP "\d+\.\d+\.\d+":string

Tools

gapseq AGPL-3.0-only

included in

maintainer

get in touch

`meta`
`:map`

`fasta`
`:file`

`medium`
`:file`

`model`

`meta`
`:map`

`*.RDS`
`:file`

`tbl`

`meta`
`:map`

`*.tbl`
`:file`

`fna`

`meta`
`:map`

`*.fna`
`:file`

`log`

`meta`
`:map`

`*.log`
`:file`

`versions_gapseq`

`${task.process}`
`:string`

`gapseq`
`:string`

`gapseq -v 2>&1 | grep -oP "\d+\.\d+\.\d+"`
`:string`

`versions`

`${task.process}`
`:string`

`gapseq`
`:string`

`gapseq -v 2>&1 | grep -oP "\d+\.\d+\.\d+"`
`:string`

gapseq
AGPL-3.0-only