diamond_blastp

Description¶

Queries a DIAMOND database using blastp mode

Keywords: fasta, diamond, blastp, DNA sequence

nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install diamond/blastp

Accelerated BLAST compatible local sequence aligner

Name	Type	Description	Pattern
`meta`	map	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`
`outfmt`	integer	Specify the type of output file to be generated. 0, .blast, BLAST pairwise format. 5, .xml, BLAST XML format. 6, .txt, BLAST tabular format (default). This format can be customized, the 6 may be followed by a space-separated list of the blast_columns keywords, each specifying a field of the output. 100, .daa, DIAMOND alignment archive (DAA). The DAA format is a proprietary binary format that can subsequently be used to generate other output formats using the view command. It is also supported by MEGAN and allows a quick import of results. 101, .sam, SAM format. 102, .tsv, Taxonomic classification. This format will not print alignments but only a taxonomic classification for each query using the LCA algorithm. 103, .paf, PAF format. The custom fields in the format are AS (bit score), ZR (raw score) and ZE (e-value).	`0\|5\|6\|100\|101\|102\|103`
`blast_columns`	string	Optional space separated list of DIAMOND tabular BLAST output keywords used in conjunction with the --outfmt 6 option (txt). Options: qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore	-

Name	Type	Pattern
`blast`	file	-
`xml`	file	-
`txt`	file	-
`daa`	file	-
`sam`	file	-
`tsv`	file	-
`paf`	file	-
`versions`	file	-

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