bwa_mem2/bwa_mem2_index

alignment

indexing

BWA

BWA-MEM

BWA-MEM2

reference

Description

Index sequences in the FASTA format for BWA alignment.

Type

bash_script

License

MIT

Keywords

alignment

indexing

BWA

BWA-MEM

BWA-MEM2

reference

Links

Repository

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output.bwa_index"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.5.0 \  
  -main-script target/nextflow/bwa_mem2/bwa_mem2_index/main.nf \  
  -params-file params.yaml

Input

Name	Type & Properties	Description
--input	file required	Input FASTA file to be indexed.

Name

Type & Properties

--input

file

required

Output

Name	Type & Properties	Description
--output	file output	Output directory containing BWA index files (.0123, .amb, .ann, .bwt.2bit.64, .pac).

Name

Type & Properties

--output

file

output

Options

Name	Type & Properties	Description
--prefix -p	string	Prefix of the index files. Default is same as input fasta name.

Name

Type & Properties

--prefix

-p

string