workflows/ingestion/make_reference

Description

Build a transcriptomics reference into one of many formats.

Type

nextflow_script

Contributors

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
id: "run"  
target: [ "star" ]  
output_fasta: "$id.$key.output_fasta.gz"  
output_gtf: "$id.$key.output_gtf.gz"  
output_cellranger: "$id.$key.output_cellranger.gz"  
output_bd_rhapsody: "$id.$key.output_bd_rhapsody.gz"  
output_star: "$id.$key.output_star.gz"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision 1.0.1 \  
  -main-script target/nextflow/workflows/ingestion/make_reference/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--id	string required	ID of the reference.
--genome_fasta	file required	Reference genome fasta.
--transcriptome_gtf	file required	Reference transcriptome annotation.
--ercc	file	ERCC sequence and annotation file.

Name

Type & Properties

--id

string

required

--genome_fasta

file

required

--transcriptome_gtf

file

required

--ercc

file

Outputs

Name	Type & Properties	Description
--target	string multiple	Which reference indices to generate.
--output_fasta	file output	Output genome sequence fasta.
--output_gtf	file output	Output transcriptome annotation gtf.
--output_cellranger	file output	Output index
--output_bd_rhapsody	file output	Output index
--output_star	file output	Output index

Name

Type & Properties

--target

string

multiple

--output_fasta

file

output

--output_gtf

file

output

--output_cellranger

file

output

--output_bd_rhapsody

file

output

--output_star

file

output

Arguments

Name	Type & Properties	Description
--subset_regex	string	Will subset the reference chromosomes using the given regex.

Name

Type & Properties

--subset_regex

string