Retrieve entries from a BLAST database
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
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
Groovy Map containing db information e.g. [ id:‘test2’, single_end:false ]
db
Input BLAST-indexed database
*.{fa.*,fasta.*}
fasta
*.fasta
Output fasta file (default format)
*.{fasta}
text
*.txt
Output text file (generic format if fasta not used, i.e. --outfmt is supplied to ext.args)
--outfmt
ext.args
*.{txt}
versions_blastdbcmd
${task.process}
The name of the process
blastdbcmd
The name of the tool
blastdbcmd -version 2>&1 | head -n1 | sed 's/^.*blastdbcmd: //; s/ .*\$//'
:eval
The expression to obtain the version of the tool
versions
BLAST finds regions of similarity between biological sequences.
