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.
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. |
Output
Name | Type & Properties | Description |
|---|---|---|
--output -f | file output | Output SAM file. If not specified, output goes to stdout. |
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'. |
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 Relationships
Used by
0 relationships
No components use this component.
Current component
bwa/bwa_samsebiobox v0.4.1
Uses
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