Description
Counts the number of alignments in SAM/BAM/CRAM files for each FLAG type.
Type
bash_script
License
MIT/Expat
Keywords
Contributors
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 v0.4.2 \
-main-script target/nextflow/samtools/samtools_flagstat/main.nf \
-params-file params.yaml Name | Type & Properties |
|---|---|
--bam | file |
--bai | file |
Name | Type & Properties |
|---|---|
--output | file required output |