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

Links

Source

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 1.0.2 -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 1.0.2 -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)