modules/blast_blastp

BLASTP (Basic Local Alignment Search Tool- Protein) compares an amino acid (protein) query sequence against a protein database

fastablastblastpprotein

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

Description

BLASTP (Basic Local Alignment Search Tool- Protein) compares an amino acid (protein) query sequence against a protein database

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 queries sequences

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

`meta2`
`:map`

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

`db`
`:directory`

Directory containing the blast database

*

`out_ext`
`:string`

Specify the type of output file to be generated. xml corresponds to BLAST xml format. tsv corresponds to BLAST tabular format. csv corresponds to BLAST comma separated format.

xml|tsv|csv

Output

name:type

description

pattern

`xml`

`meta`
`:map`

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

`.xml`
`:file`

File containing blastp hits in XML format

*.{xml}

`tsv`

`meta`
`:map`

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

`.tsv`
`:file`

File containing blastp hits in tabular format

*.{tsv}

`csv`

`meta`
`:map`

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

`.csv`
`:file`

File containing blastp hits in comma separated format

*.csv

`versions_blastp`

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

The name of the process

`blastp`
`:string`

The name of the tool

`blastp -version 2>&1 | sed 's/^.blastp: //; s/ .\$//'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`blastp`
`:string`

The name of the tool

`blastp -version 2>&1 | sed 's/^.blastp: //; s/ .\$//'`
`:eval`

The expression to obtain the version of the tool

Tools

blast
US-Government-Work

BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ Toolkit.

blast.ncbi.nlm.nih.gov/Blast.cgi blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs 10.1016/S0022-2836(05)80360-2

modules/blast_blastp

Description

Input

`meta`
`:map`

`fasta`
`:file`

`meta2`
`:map`

`db`
`:directory`

`out_ext`
`:string`

Output

`xml`

`meta`
`:map`

`.xml`
`:file`

`tsv`

`meta`
`:map`

`.tsv`
`:file`

`csv`

`meta`
`:map`

`.csv`
`:file`

`versions_blastp`

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

`blastp`
`:string`

`blastp -version 2>&1 | sed 's/^.blastp: //; s/ .\$//'`
`:eval`

Topics

`versions`

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

`blastp`
`:string`

`blastp -version 2>&1 | sed 's/^.blastp: //; s/ .\$//'`
`:eval`

Tools

blast
US-Government-Work

maintainer

get in touch

modules/blast_blastp

Description

Input

meta:map

fasta:file

meta2:map

db:directory

out_ext:string

Output

xml

meta:map

*.xml*:file

tsv

meta:map

*.tsv*:file

csv

meta:map

*.csv*:file

versions_blastp

${task.process}:string

blastp:string

blastp -version 2>&1 | sed 's/^.*blastp: //; s/ .*\$//':eval

Topics

versions

${task.process}:string

blastp:string

blastp -version 2>&1 | sed 's/^.*blastp: //; s/ .*\$//':eval

Tools

blast US-Government-Work

maintainer

get in touch

`meta`
`:map`

`fasta`
`:file`

`meta2`
`:map`

`db`
`:directory`

`out_ext`
`:string`

`xml`

`meta`
`:map`

`.xml`
`:file`

`tsv`

`meta`
`:map`

`.tsv`
`:file`

`csv`

`meta`
`:map`

`.csv`
`:file`

`versions_blastp`

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

`blastp`
`:string`

`blastp -version 2>&1 | sed 's/^.blastp: //; s/ .\$//'`
`:eval`

`versions`

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

`blastp`
`:string`

`blastp -version 2>&1 | sed 's/^.blastp: //; s/ .\$//'`
`:eval`

blast
US-Government-Work