bwa/bwa_samse

alignment

BWA

BWA-samse

SAM

single-end

Description

BWA samse - generate single-end alignment in SAM format from BWA aln SAI files.

Type

bash_script

License

MIT

Keywords

alignment

BWA

BWA-samse

SAM

single-end

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.sam"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.1 \  
  -main-script target/nextflow/bwa/bwa_samse/main.nf \  
  -params-file params.yaml

Input

Name	Type & Properties	Description
--index	file required	BWA index base name (prefix of .amb, .ann, .bwt, .pac, .sa files).
--sai	file required	Input SAI file generated by BWA aln.
--reads	file required	Input FASTQ file with single-end reads.

Name

Type & Properties

--index

file

required

--sai

file

required

--reads

file

required

Output

Name	Type & Properties	Description
--output -f	file output	Output SAM file. If not specified, output goes to stdout.

Name

Type & Properties

--output

-f

file

output

Options

Name	Type & Properties	Description
--max_occ -n	integer	Maximum occurrences for read mapping. Default varies by BWA version.
--read_group -r	string	Read group header line such as '@RG\tID:foo\tSM:bar'.

Name

Type & Properties

--max_occ

-n

integer

--read_group

-r

string