Nextflow Registry | nf-core/diamond/blastx@0.0.0-6c4ed3a

nf-core/diamond/blastx @ 0.0.0-6c4ed3a

Queries a DIAMOND database using blastx mode

fasta diamond blastx DNA sequence

Latest version: 0.0.0-6c4ed3a

Total downloads: 10

Source: nf-core/modules

Authors: @spficklin @jfy133 @mjamy

Maintainers: @spficklin @jfy133 @mjamy @vagkaratzas

Queries a DIAMOND database using blastx mode

Add the following snippet to your workflow script to include this module.

include { DIAMOND_BLASTX } from 'nf-core/diamond/blastx'

MIT License

Process

`Name`	`DIAMOND_BLASTX`

Input 4 channels

#1 tuple

`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}`

#2 tuple

`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 9 channels

#1 daa tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.daa` file	File containing hits DAA format `*.{daa}`

#2 log tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.log` file	Log file containing stdout information `*.{log}`

#3 paf tuple

`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}`

#4 sam tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.sam` file	File containing aligned reads in SAM format `*.{sam}`

#5 tsv tuple

`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}`

#6 txt tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.txt` file	File containing hits in tabular BLAST format. `*.{txt}`

#7 xml tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.xml` file	File containing blastp hits `*.{xml}`

#8 blast tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.blast` file	File containing blastp hits `*.{blast}`

#9 versions_diamond tuple

`${task.process}` string	The name of the process
`diamond` string	The name of the tool