cat_additional_fasta

Description

Concatenate addional fasta file to reference FASTA and GTF files.

Type

python_script

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
fasta_output: "$id.$key.fasta_output"  
gtf_output: "$id.$key.gtf_output"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/rnaseq.git \  
  -revision v0.3.0 \  
  -main-script target/nextflow/cat_additional_fasta/main.nf \  
  -params-file params.yaml

Input

Name	Type & Properties	Description
--fasta	file required	Path to FASTA genome file.
--gtf	file	Path to GTF annotation file.
--additional_fasta	file	FASTA file to concatenate to genome FASTA file e.g. containing spike-in sequences.
--biotype	string	Biotype value to use when appending entries to GTF file when additional fasta file is provided.

Name

Type & Properties

--fasta

file

required

--gtf

file

--additional_fasta

file

--biotype

string

Output

Name	Type & Properties	Description
--fasta_output	file output	Concatenated FASTA file.
--gtf_output	file output	Concatenated GTF file.

Name

Type & Properties

--fasta_output

file

output

--gtf_output

file

output