modules/interproscan

Produces protein annotations and predictions from an amino acids FASTA file

annotationfastaproteindnainterproscan

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

Description

Produces protein annotations and predictions from an amino acids FASTA file

Input

name:type

description

pattern

`meta`
`:map`

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

`fasta`
`:file`

Input fasta file containing the amino acid or dna query sequences

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

`interproscan_database`
`:directory`

Path to the data/ folder of an InterProScan release matching the module version (untarred from http://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/${version_major}-${version_minor}/interproscan-${version_major}-${version_minor}-64-bit.tar.gz). HMMs should already be pressed (python3 setup.py -f interproscan.properties), otherwise hmmpress runs in every task and parallel tasks may race.

Output

name:type

description

pattern

`tsv`

`meta`
`:map`

Groovy Map containing sample information

`*.tsv`
`:file`

Tab separated file containing with detailed hits

*.{tsv}

`xml`

`meta`
`:map`

Groovy Map containing sample information

`*.xml`
`:file`

XML file containing with detailed hits

*.{xml}

`gff3`

`meta`
`:map`

Groovy Map containing sample information

`*.gff3`
`:file`

GFF3 file containing with detailed hits

*.{gff3}

`json`

`meta`
`:map`

Groovy Map containing sample information

`*.json`
`:file`

JSON file containing with detailed hits

*.{json}

`versions_interproscan`

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

The name of the process

`interproscan`
`:string`

The name of the tool

`interproscan.sh --version | sed "1!d; s/.*version //"`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`interproscan`
`:string`

The name of the tool

`interproscan.sh --version | sed "1!d; s/.*version //"`
`:eval`

The expression to obtain the version of the tool

Tools

interproscan
GPL v3

InterPro integrates together predictive information about proteins function from a number of partner resources

ebi.ac.uk/interpro/search/sequence interproscan-docs.readthedocs.io https://github.com/ebi-pf-team/interproscan 10.1093/bioinformatics/btu031

modules/interproscan

Description

Input

`meta`
`:map`

`fasta`
`:file`

`interproscan_database`
`:directory`

Output

`tsv`

`meta`
`:map`

`*.tsv`
`:file`

`xml`

`meta`
`:map`

`*.xml`
`:file`

`gff3`

`meta`
`:map`

`*.gff3`
`:file`

`json`

`meta`
`:map`

`*.json`
`:file`

`versions_interproscan`

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

`interproscan`
`:string`

`interproscan.sh --version | sed "1!d; s/.*version //"`
`:eval`

Topics

`versions`

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

`interproscan`
`:string`

`interproscan.sh --version | sed "1!d; s/.*version //"`
`:eval`

Tools

interproscan
GPL v3

included in

maintainers

get in touch

modules/interproscan

Description

Input

meta :map

fasta :file

interproscan_database :directory

Output

tsv

meta :map

*.tsv :file

xml

meta :map

*.xml :file

gff3

meta :map

*.gff3 :file

json

meta :map

*.json :file

versions_interproscan

${task.process} :string

interproscan :string

interproscan.sh --version | sed "1!d; s/.*version //" :eval

Topics

versions

${task.process} :string

interproscan :string

interproscan.sh --version | sed "1!d; s/.*version //" :eval

Tools

interproscanGPL v3

included in

maintainers

get in touch

`meta`
`:map`

`fasta`
`:file`

`interproscan_database`
`:directory`

`tsv`

`meta`
`:map`

`*.tsv`
`:file`

`xml`

`meta`
`:map`

`*.xml`
`:file`

`gff3`

`meta`
`:map`

`*.gff3`
`:file`

`json`

`meta`
`:map`

`*.json`
`:file`

`versions_interproscan`

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

`interproscan`
`:string`

`interproscan.sh --version | sed "1!d; s/.*version //"`
`:eval`

`versions`

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

`interproscan`
`:string`

`interproscan.sh --version | sed "1!d; s/.*version //"`
`:eval`

interproscan
GPL v3