Queries a BLAST DNA database
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
fasta{:bash}
:file
Input fasta file containing queries sequences
*.{fa,fasta,fa.gz,fasta.gz}
meta2{:bash}
Groovy Map containing db information e.g. [ id:‘test2’, single_end:false ]
db{:bash}
:directory
Directory containing the blast database
*
taxidlist{:bash}
File containing NCBI taxon ids, one per line, for filtering the database.
*.{txt}
taxids{:bash}
:string
Comma-delimited list of NCBI taxon ids for filtering the database.
^[0-9]+(,[0-9]+)*$
negative_tax{:bash}
:boolean
Use negative filtering (true) to exclude taxon ids or normal filtering (false).
true or false
txt{:bash}
*.txt{:bash}
File containing blastn hits
*.txt
versions_blastn{:bash}
${task.process}{:bash}
The name of the process
blastn{:bash}
The name of the tool
blastn -version 2>&1 | sed 's/^.*blastn: //; s/ .*\$//'{:bash}
:eval
The expression to obtain the version of the tool
versions{:bash}
BLAST finds regions of similarity between biological sequences.
