Viash Hub

Description

Counts the number of alignments in SAM/BAM/CRAM files for each FLAG type.

Inputs

Name	Type & Properties	Description
--bam	file	BAM input files.
--bai	file	BAM index file.

Name

Type & Properties

--bam

file

--bai

file

Outputs

Name	Type & Properties	Description
--output	file required output	File containing samtools stats output.

Name

Type & Properties

--output

file

required

output

Run this component

Run the following command to execute this component with Nextflow:

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

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

Relationships

Used by

0 relationships

No components use this component.

Current component

samtools/samtools_flagstatbiobox v0.3.0

Uses

0 relationships

No component dependencies found.