Search for protein structural hits against a foldseek database of protein structures
meta
:map
Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
[ 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
Groovy Map containing sample information for the foldseek db e.g. [ id:'test', single_end:false ]
db
:directory
foldseek database from protein structures
*
aln
${prefix}.m8
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
The name of the tool
foldseek --help |& sed -n 's/.*Version: //p'
:eval
The expression to obtain the version of the tool
versions
Foldseek: fast and accurate protein structure search
