modules/foldseek_easysearch

Search for protein structural hits against a foldseek database of protein structures

proteinstructurecomparisons

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

Description

Search for protein structural hits against a foldseek database of protein structures

Input

name:type

description

pattern

`meta`
`:map`

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

`pdb`
`:file`

Protein structure(s) in PDB, mmCIF or mmJSON format to compare against a foldseek database (also works with folder input)

*.{pdb,mmcif,mmjson}

`meta2`
`:map`

Groovy Map containing sample information for the foldseek db e.g. [ id:'test', single_end:false ] If ${db}/${meta2.id}.dbtype exists, meta2.id selects the database within the directory; otherwise it is ignored and the database is auto-discovered via the single .lookup file in the directory (fails if zero or several are found)

`db`
`:directory`

Foldseek database directory built from protein structures

*

Output

name:type

description

pattern

`aln`

`meta`
`:map`

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

`${prefix}.m8`
`:file`

Structural comparisons file output Query, Target, Identity, Alignment length, Mismatches, Gap openings, Query start, Query end, Target start, Target end, E-value, Bit score

*.{m8}

`versions_foldseek`

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

The name of the process

`foldseek`
`:string`

The name of the tool

`foldseek --help |& sed -n 's/.*Version: //p'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`foldseek`
`:string`

The name of the tool

`foldseek --help |& sed -n 's/.*Version: //p'`
`:eval`

The expression to obtain the version of the tool

Tools

foldseek
GPL v3

Foldseek: fast and accurate protein structure search

search.foldseek.com/search github.com/steineggerlab/foldseek 10.1038/s41587-023-01773-0

modules/foldseek_easysearch

Description

Input

`meta`
`:map`

`pdb`
`:file`

`meta2`
`:map`

`db`
`:directory`

Output

`aln`

`meta`
`:map`

`${prefix}.m8`
`:file`

`versions_foldseek`

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

`foldseek`
`:string`

`foldseek --help |& sed -n 's/.*Version: //p'`
`:eval`

Topics

`versions`

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

`foldseek`
`:string`

`foldseek --help |& sed -n 's/.*Version: //p'`
`:eval`

Tools

foldseek
GPL v3

included in

maintainer

get in touch

modules/foldseek_easysearch

Description

Input

meta :map

pdb :file

meta2 :map

db :directory

Output

aln

meta :map

${prefix}.m8 :file

versions_foldseek

${task.process} :string

foldseek :string

foldseek --help |& sed -n 's/.*Version: //p' :eval

Topics

versions

${task.process} :string

foldseek :string

foldseek --help |& sed -n 's/.*Version: //p' :eval

Tools

foldseekGPL v3

included in

maintainer

get in touch

`meta`
`:map`

`pdb`
`:file`

`meta2`
`:map`

`db`
`:directory`

`aln`

`meta`
`:map`

`${prefix}.m8`
`:file`

`versions_foldseek`

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

`foldseek`
`:string`

`foldseek --help |& sed -n 's/.*Version: //p'`
`:eval`

`versions`

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

`foldseek`
`:string`

`foldseek --help |& sed -n 's/.*Version: //p'`
`:eval`

foldseek
GPL v3