From bd to 10x molecular barcode tags

Convert the molecular barcode sequence SAM tag from BD format (MA) to 10X format (UB)

Info

ID: from_bd_to_10x_molecular_barcode_tags
Namespace: convert

Example commands

You can run the pipeline using nextflow run.

View help

You can use --help as a parameter to get an overview of the possible parameters.

nextflow run openpipelines-bio/openpipeline \
  -r 0.12.6 -latest \
  -main-script target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/main.nf \
  --help

Run command

Example of params.yaml
# Arguments
input: # please fill in - example: "input.bam"
# output: "$id.$key.output.sam"
bam: false
# threads: 123

# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"
nextflow run openpipelines-bio/openpipeline \
  -r 0.12.6 -latest \
  -profile docker \
  -main-script target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/main.nf \
  -params-file params.yaml
Note

Replace -profile docker with -profile podman or -profile singularity depending on the desired backend.

Argument group

Arguments

Name Description Attributes
--input Input SAM or BAM file. file, required, example: "input.bam"
--output Output alignment file. file, example: "output.sam"
--bam Output a BAM file. boolean_true
--threads Number of threads integer

Authors

  • Dries Schaumont (maintainer)