samtools/samtools_index

index

bam

sam

cram

Description

Index SAM/BAM/CRAM files.

Type

bash_script

License

MIT/Expat

Keywords

index

bam

sam

cram

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

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.2 \  
  -main-script target/nextflow/samtools/samtools_index/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input	file required	Input file name

Name

Type & Properties

--input

file

required

Outputs

Name	Type & Properties	Description
--output -o	file required output	Output file name

Name

Type & Properties

--output

-o

file

required

output

Options

Name	Type & Properties	Description
--bai -b	boolean_true	Generate BAM index
--csi -c	boolean_true	Create a CSI index for BAM files instead of the traditional BAI index. This will be required for genomes with larger chromosome sizes.
--min_shift -m	integer	Create a CSI index, with a minimum interval size of 2^INT.

Name

Type & Properties

--bai

-b

boolean_true

--csi

-c

boolean_true

--min_shift

-m

integer