Velocyto

Runs the velocity analysis on a BAM file, outputting a loom file.

Info

ID: velocyto
Namespace: velocity

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/velocity/velocyto/main.nf \
  --help

Run command

Example of params.yaml

# Arguments
input: # please fill in - example: "path/to/file"
transcriptome: # please fill in - example: "path/to/file"
# barcode: "path/to/file"
without_umi: false
# output: "$id.$key.output.output"
logic: "Default"

# 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/velocity/velocyto/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	Path to BAM file	file, required
--transcriptome	Path to GTF file	file, required
--barcode	Valid barcodes file, to filter the bam. If –bcfile is not specified all the cell barcodes will be included. Cell barcodes should be specified in the bcfile as the ‘CB’ tag for each read	file
--without_umi	foo	boolean_true
--output	Velocyto loom file	file, required
--logic	The logic to use for the filtering.	string, default: "Default"

Authors

• Robrecht Cannoodt (maintainer)