samtools/samtools_index
index
bam
sam
cram
Description
Index SAM/BAM/CRAM files.
Inputs
Name | Type & Properties | Description |
|---|---|---|
--input | file required | Input file name |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output -o | file required output | Output file name |
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. |
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 Relationships
Used by
0 relationships
No components use this component.
Current component
samtools/samtools_indexbiobox v0.4.2
Uses
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No component dependencies found.