bwa/bwa_index

alignment

indexing

BWA

reference

Description

Index sequences in the FASTA format for BWA alignment.

Type

bash_script

License

MIT

Keywords

alignment

indexing

BWA

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 v0.4.2 \  
  -main-script target/nextflow/bwa/bwa_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 (.amb, .ann, .bwt, .pac, .sa).

Name

Type & Properties

--output

file

output

Options

Name	Type & Properties	Description
--algorithm -a	string	BWT construction algorithm. If not specified, BWA will choose automatically.
--prefix -p	string	Prefix of the index files. Default is same as input fasta name.
--block_size -b	integer	Block size for the bwtsw algorithm (effective with -a bwtsw). Default is 10000000.
--use_64bit_names -6	boolean_true	Index files named as <in.fasta>.64.* instead of <in.fasta>.*.

Name

Type & Properties

--algorithm

-a

string

--prefix

-p

string

--block_size

-b

integer

--use_64bit_names

-6

boolean_true