bedtools/bedtools_bamtofastq

Conversion

BAM

FASTQ

Description

Conversion tool for extracting FASTQ records from sequence alignments in BAM format.

Type

bash_script

License

MIT

Keywords

Conversion

BAM

FASTQ

Links

Repository

Issues

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
fastq: "$id.$key.fastq"  
fastq2: "$id.$key.fastq2"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.2.0 \  
  -main-script target/nextflow/bedtools/bedtools_bamtofastq/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input -i	file required	Input BAM file to be converted to FASTQ.

Name

Type & Properties

--input

-i

file

required

Outputs

Name	Type & Properties	Description
--fastq -fq	file required output	Output FASTQ file.
--fastq2 -fq2	file output	FASTQ for second end. Used if BAM contains paired-end data. BAM should be sorted by query name is creating paired FASTQ.

Name

Type & Properties

--fastq

-fq

file

required

output

--fastq2

-fq2

file

output

Options

Name	Type & Properties	Description
--tags	boolean_true	Create FASTQ based on the mate info in the BAM R2 and Q2 tags.

Name

Type & Properties

--tags

boolean_true