modules/carveme_carve

Reconstruct genome-scale metabolic models from protein FASTA files using CarveMe

metabolic modelgenome-scalesbmlflux balance analysismetabolic reconstruction

https://github.com/nf-core/modules/[...]/modules/nf-core/carveme/carve

Description

Reconstruct genome-scale metabolic models from protein FASTA files using CarveMe

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`fasta`
`:file`

Protein FASTA file or DNA fasta file if the —dna flag is provided

*.{fa,faa,fasta,fna}

`universe_file`
`:file`

Optional. Reaction universe file in SBML format, passed to —universe-file.

*.xml

`mediadb`
`:file`

Optional. Media database file, passed to —mediadb. —gapfill X,Y,Z with medium names from the database must also be provided

*.{tsv,csv,txt}

`soft`
`:file`

Optional. Soft constraints file, passed to —soft.

*.{tsv,csv,txt}

`hard`
`:file`

Optional. Hard constraints file, passed to —hard.

*.{tsv,csv,txt}

`reference`
`:file`

Optional. Manually curated model of a close reference species, passed to —reference.

*.xml

Output

name:type

description

pattern

`model`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`${prefix}.xml`
`:file`

SBML genome-scale metabolic model file

*.xml

`gene_scores`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`${prefix}_gene_scores.tsv`
`:file`

Optional. Tab-separated file produced when —debug is passed. Maps each query gene to its corresponding BiGG gene identifier, protein group, reaction, source model, and BLAST bit-score used during model reconstruction.

*_gene_scores.tsv

`milp_problem`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`${prefix}_milp_problem.lp`
`:file`

Optional. Linear programming problem file in LP format produced when —debug is passed. Contains the MILP formulation (variables, constraints, and objective function) passed to the SCIP solver during gap-filling or reaction selection.

*_milp_problem.lp

`milp_solution`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`${prefix}_milp_solution.tsv`
`:file`

Optional. Tab-separated file produced when —debug is passed. Contains the MILP solver solution, listing each reaction identifier and its corresponding flux value selected during model gap-filling.

*_milp_solution.tsv

`protein_scores`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`${prefix}_protein_scores.tsv`
`:file`

Optional. Tab-separated file produced when —debug is passed. Lists the BLAST alignment scores for each query protein against the template model database, including the matched protein group, reaction, source model, and GPR rule used for scoring.

*_protein_scores.tsv

`reaction_scores`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`${prefix}_reaction_scores.tsv`
`:file`

Optional. Tab-separated file produced when —debug is passed. Lists each candidate reaction with its GPR rule, raw BLAST bit-score, and normalised score used to weight the MILP objective during model reconstruction.

*_reaction_scores.tsv

`versions_carveme`

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

The name of the process

`carveme`
`:string`

The name of the tool

`pip show carveme | sed -n 's/^Version: //p'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`carveme`
`:string`

The name of the tool

`pip show carveme | sed -n 's/^Version: //p'`
`:eval`

The expression to obtain the version of the tool

Tools

carveme
Apache-2.0

CarveMe is a python-based tool for genome-scale metabolic model reconstruction.

carveme.readthedocs.io https://github.com/cdanielmachado/carveme 10.1093/nar/gky537

modules/carveme_carve

Description

Input

meta:map

fasta:file

universe_file:file

mediadb:file

soft:file

hard:file

reference:file

Output

model

meta:map

${prefix}.xml:file

gene_scores

meta:map

${prefix}_gene_scores.tsv:file

milp_problem

meta:map

${prefix}_milp_problem.lp:file

milp_solution

meta:map

${prefix}_milp_solution.tsv:file

protein_scores

meta:map

${prefix}_protein_scores.tsv:file

reaction_scores

meta:map

${prefix}_reaction_scores.tsv:file

versions_carveme

${task.process}:string

carveme:string

pip show carveme | sed -n 's/^Version: //p':eval

Topics

versions

${task.process}:string

carveme:string

pip show carveme | sed -n 's/^Version: //p':eval

Tools

carveme Apache-2.0

included in

maintainer

get in touch

`meta`
`:map`

`fasta`
`:file`

`universe_file`
`:file`

`mediadb`
`:file`

`soft`
`:file`

`hard`
`:file`

`reference`
`:file`

`model`

`meta`
`:map`

`${prefix}.xml`
`:file`

`gene_scores`

`meta`
`:map`

`${prefix}_gene_scores.tsv`
`:file`

`milp_problem`

`meta`
`:map`

`${prefix}_milp_problem.lp`
`:file`

`milp_solution`

`meta`
`:map`

`${prefix}_milp_solution.tsv`
`:file`

`protein_scores`

`meta`
`:map`

`${prefix}_protein_scores.tsv`
`:file`

`reaction_scores`

`meta`
`:map`

`${prefix}_reaction_scores.tsv`
`:file`

`versions_carveme`

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

`carveme`
`:string`

`pip show carveme | sed -n 's/^Version: //p'`
`:eval`

`versions`

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

`carveme`
`:string`

`pip show carveme | sed -n 's/^Version: //p'`
`:eval`

carveme
Apache-2.0