nf-core/diamond/blastp @ 0.0.0-6c4ed3a
Summary
Queries a DIAMOND database using blastp mode
Get started
Add the following snippet to your workflow script to include this module.
include { DIAMOND_BLASTP } from 'nf-core/diamond/blastp'
License
MIT License
Name
|
DIAMOND_BLASTP |
|---|
meta
map
|
Groovy Map containing sample information e.g. [ id:'test' ] |
|---|---|
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' ] |
|---|---|
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 |
|---|
daa
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', db:'ncbi-refseq' ] |
|---|---|
*.{daa,daa.gz}
file
|
File containing hits DAA format *.{daa,daa.gz}
|
paf
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', db:'ncbi-refseq' ] |
|---|---|
*.{paf,paf.gz}
file
|
File containing aligned reads in pairwise mapping format format *.{paf,paf.gz}
|
sam
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', db:'ncbi-refseq' ] |
|---|---|
*.{sam,sam.gz}
file
|
File containing aligned reads in SAM format *.{sam,sam.gz}
|
tsv
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', db:'ncbi-refseq' ] |
|---|---|
*.{tsv,tsv.gz}
file
|
Tab separated file containing taxonomic classification of hits *.{tsv,tsv.gz}
|
txt
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', db:'ncbi-refseq' ] |
|---|---|
*.{txt,txt.gz}
file
|
File containing hits in tabular BLAST format. *.{txt,txt.gz}
|
xml
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', db:'ncbi-refseq' ] |
|---|---|
*.{xml,xml.gz}
file
|
File containing blastp hits *.{xml,xml.gz}
|
blast
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', db:'ncbi-refseq' ] |
|---|---|
*.{blast,blast.gz}
file
|
File containing blastp hits *.{blast,blast.gz}
|
versions_diamond
tuple
${task.process}
string
|
The name of the process |
|---|---|
diamond
string
|
The name of the tool |
diamond --version 2>&1 | tail -n 1 | sed "s/^diamond version //"
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|