Description

Queries a BLAST DNA database from a FASTA/FASTQ/BAM/CRAM file containing query sequences.

Input

Name
Description
Pattern

meta (map)

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

input (file)

Input FASTA/FASTQ/BAM/CRAM file containing queries sequences

*.{fa,fasta,fa.gz,fasta.gz,bam,cram,fastq,fq,fastq.gz,fq.gz}

meta2 (map)

Groovy Map containing db information e.g. [ id:'test2', single_end:false ]

db (directory)

Directory containing the blast database

*

taxidlist (file)

File containing NCBI taxon ids, one per line, for filtering the database.

*.{txt}

taxids (string)

Comma-delimited list of NCBI taxon ids for filtering the database.

^[0-9]+(,[0-9]+)*$

negative_tax (boolean)

Use negative filtering (true) to exclude taxon ids or normal filtering (false).

true or false

Output

Name
Description
Pattern

txtgz

meta (map)

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

*.txt.gz (file)

gzipped file containing blastn hits

*.txt.gz

versions_blast

${task.process} (string)

Name of the process

blastn (string)

The name of the tool

blastn -version 2>&1 | sed "s/^.*blastn: //; s/ .*$//" (eval)

The expression to obtain the version of the tool

versions_seqkit

${task.process} (string)

Name of the process

seqkit (string)

The name of the tool

seqkit | sed "3!d; s/Version: //" (eval)

The expression to obtain the version of the tool

versions_samtools

${task.process} (string)

Name of the process

samtools (string)

Name of the tool

samtools --version | head -1 | sed -e "s/samtools //" (eval)

The expression to obtain the version of the tool

Topics

Name
Description
Pattern

versions

${task.process} (string)

Name of the process

blastn (string)

The name of the tool

blastn -version 2>&1 | sed "s/^.*blastn: //; s/ .*$//" (eval)

The expression to obtain the version of the tool

${task.process} (string)

Name of the process

samtools (string)

Name of the tool

samtools --version | head -1 | sed -e "s/samtools //" (eval)

The expression to obtain the version of the tool

${task.process} (string)

Name of the process

seqkit (string)

The name of the tool

seqkit | sed "3!d; s/Version: //" (eval)

The expression to obtain the version of the tool

Tools

blast Documentation

BLAST finds regions of similarity between biological sequences.

doi: 10.1016/S0022-2836(05)80360-2License: US-Government-Work

samtools Documentation

SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.

doi: 10.1093/bioinformatics/btp352License: MIT

seqkit Documentation

Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.

doi: 10.1371/journal.pone.0163962License: MIT
Authors