Description

Retrieve entries from a BLAST database

Input

name:type
description
pattern

meta:map

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

]

entry:string

Entry identifier of sequence in database. It cannot be used along with entry_batch

entry_batch:file

File with a list of entry identifiers of sequences in database (one identifier per line). It cannot be used along with entry

meta2:map

Groovy Map containing db information e.g. [ id:‘test2’, single_end

]

db:file

Input BLAST-indexed database

*.{fa.*,fasta.*}

Output

name:type
description
pattern

fasta

meta:map

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

]

*.fasta:file

Output fasta file (default format)

*.{fasta}

text

meta:map

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

]

*.txt:file

Output text file (generic format if fasta not used, i.e. --outfmt is supplied to ext.args)

*.{txt}

versions

versions.yml:file

File containing software versions

versions.yml

Tools

blast
US-Government-Work

BLAST finds regions of similarity between biological sequences.