rseqc/rseqc_bamstat

rnaseq

genomics

Description

Generate statistics from a bam file.

Type

bash_script

License

GPL-3.0

Keywords

rnaseq

genomics

Links

Repository

Issues

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

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

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.3.0 \  
  -main-script target/nextflow/rseqc/rseqc_bamstat/main.nf \  
  -params-file params.yaml

Input

Name	Type & Properties	Description
--input_file -i	file required	Input alignment file in BAM or SAM format.
--mapq -q	integer	Minimum mapping quality (phred scaled) to determine uniquely mapped reads. Default: '30'.

Name

Type & Properties

--input_file

-i

file

required

--mapq

-q

integer

Output

Name	Type & Properties	Description
--output	file output	Output file (txt) with mapping quality statistics.

Name

Type & Properties

--output

file

output