reference/make_reference

Description

Preprocess and build a transcriptome reference.

Example input files are:

genome_fasta: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_41/GRCh38.primary_assembly.genome.fa.gz
transcriptome_gtf: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_41/gencode.v41.annotation.gtf.gz
ercc: https://assets.thermofisher.com/TFS-Assets/LSG/manuals/ERCC92.zip

Arguments

Name	Type & Properties	Description
--genome_fasta	file required	Reference genome fasta. Example:
--transcriptome_gtf	file required	Reference transcriptome annotation.
--ercc	file	ERCC sequence and annotation file.
--subset_regex	string	Will subset the reference chromosomes using the given regex.
--output_fasta	file required output	Output genome sequence fasta.
--output_gtf	file required output	Output transcriptome annotation gtf.

Name

Type & Properties

--genome_fasta

file

required

--transcriptome_gtf

file

required

--ercc

file

--subset_regex

string

--output_fasta

file

required

output

--output_gtf

file

required

output

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output_fasta: "$id.$key.output_fasta.gz"  
output_gtf: "$id.$key.output_gtf.gz"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.2.0 \  
  -main-script target/nextflow/reference/make_reference/main.nf \  
  -params-file params.yaml

reference/make_reference

Arguments

Run this component

Relationships

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Uses