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
xml
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.xml
:file
Gap-filled metabolic model in SBML XML format
*.xml
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.
