velocity/velocyto

Description

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

Type

bash_script

Contributors

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output"  
logic: [ "Default" ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision 1.0.2 \  
  -main-script target/nextflow/velocity/velocyto/main.nf \  
  -params-file params.yaml

Arguments

Name	Type & Properties	Description
--input -i	file required	Path to BAM file
--transcriptome -t	file required	Path to GTF file
--barcode -b	file	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
--without_umi	boolean_true	foo
--output -o	file required output	Velocyto loom file
--logic -l	string	The logic to use for the filtering.

Name

Type & Properties

--input

-i

file

required

--transcriptome

-t

file

required

--barcode

-b

file

--without_umi

boolean_true

--output

-o

file

required

output

--logic

-l

string