Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
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:false ]
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:false ]
*.blast:file
File containing blastp hits
*.{blast}
xml
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.xml:file
File containing blastp hits
*.{xml}
txt
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.txt:file
File containing hits in tabular BLAST format.
*.{txt}
daa
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.daa:file
File containing hits DAA format
*.{daa}
sam
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.sam:file
File containing aligned reads in SAM format
*.{sam}
tsv
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.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:false ]
*.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:false ]
*.log:file
Log file containing stdout information
*.{log}
versions
versions.yml:file
File containing software versions
versions.yml
Tools
diamond
GPL v3.0
Accelerated BLAST compatible local sequence aligner
