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

blast

meta:map

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

]

*.blast:file

File containing blastp hits

*.{blast}

xml

meta:map

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

]

*.xml:file

File containing blastp hits

*.{xml}

txt

meta:map

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

]

*.txt:file

File containing hits in tabular BLAST format.

*.{txt}

daa

meta:map

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

]

*.daa:file

File containing hits DAA format

*.{daa}

sam

meta:map

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

]

*.sam:file

File containing aligned reads in SAM format

*.{sam}

tsv

meta:map

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

]

*.tsv:file

Tab separated file containing taxonomic classification of hits

*.{tsv}

paf

meta:map

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

]

*.paf:file

File containing aligned reads in pairwise mapping format format

*.{paf}

log

meta:map

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

]

*.log:file

Log file containing stdout information

*.{log}

versions

versions.yml:file

File containing software versions

versions.yml