Description

Queries a DIAMOND database using blastx mode

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

fasta (file)

Input fasta file containing query sequences

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

meta2 (map)

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

]

db (file)

File of the indexed DIAMOND database

*.dmnd

out_ext (string)

Specify the type of output file to be generated. blast corresponds to
BLAST pairwise format. xml corresponds to BLAST xml format.
txt corresponds to to BLAST tabular format. tsv corresponds to
taxonomic classification format.

blast|xml|txt|daa|sam|tsv|paf

blast_columns (string)

Optional space separated list of DIAMOND tabular BLAST output keywords
used for in conjunction with the ‘txt’ out_ext option (—outfmt 6). Options:
qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

blast (file)

File containing blastp hits

*.{blast}

xml (file)

File containing blastp hits

*.{xml}

txt (file)

File containing hits in tabular BLAST format.

*.{txt}

daa (file)

File containing hits DAA format

*.{daa}

sam (file)

File containing aligned reads in SAM format

*.{sam}

tsv (file)

Tab separated file containing taxonomic classification of hits

*.{tsv}

paf (file)

File containing aligned reads in pairwise mapping format format

*.{paf}

log (file)

Log file containing stdout information

*.{log}

versions (file)

File containing software versions

versions.yml
included in
taxprofiler
maintainers
Github user spficklin
Github user jfy133
Github user mjamy
Github user vagkaratzas
get in touch
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