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

]

`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 interproscan database (untarred http://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/${version_major}-${version_minor}/interproscan-${version_major}-${version_minor}-64-bit.tar.gz)

Output

name:type

description

pattern

`tsv`

`meta:file`

Tab separated file containing with detailed hits

*.{tsv}

`*.tsv:file`

Tab separated file containing with detailed hits

*.{tsv}

`xml`

`meta:file`

XML file containing with detailed hits

*.{xml}

`*.xml:file`

XML file containing with detailed hits

*.{xml}

`gff3`

`meta:file`

GFF3 file containing with detailed hits

*.{gff3}

`*.gff3:file`

GFF3 file containing with detailed hits

*.{gff3}

`json`

`meta:file`

JSON file containing with detailed hits

*.{json}

`*.json:file`

JSON file containing with detailed hits

*.{json}

`versions`

`versions.yml:file`

File containing software versions

versions.yml

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:file`

`*.tsv:file`

`xml`

`meta:file`

`*.xml:file`

`gff3`

`meta:file`

`*.gff3:file`

`json`

`meta:file`

`*.json:file`

`versions`

`versions.yml:file`

Tools

interproscan
GPL v3

maintainers

get in touch

modules/interproscan

Description

Input

meta:map

fasta:file

interproscan_database:directory

Output

tsv

meta:file

*.tsv:file

xml

meta:file

*.xml:file

gff3

meta:file

*.gff3:file

json

meta:file

*.json:file

versions

versions.yml:file

Tools

interproscan GPL v3

maintainers

get in touch

`meta:map`

`fasta:file`

`interproscan_database:directory`

`tsv`

`meta:file`

`*.tsv:file`

`xml`

`meta:file`

`*.xml:file`

`gff3`

`meta:file`

`*.gff3:file`

`json`

`meta:file`

`*.json:file`

`versions`

`versions.yml:file`

interproscan
GPL v3