stringtie

Description

Transcript assembly and quantification for RNA-Seq

Type

bash_script

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
transcript_gtf: "$id.$key.transcript_gtf"  
coverage_gtf: "$id.$key.coverage_gtf"  
abundance: "$id.$key.abundance"  
ballgown: "$id.$key.ballgown"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/rnaseq.git \  
  -revision v0.1.1 \  
  -main-script target/nextflow/stringtie/main.nf \  
  -params-file params.yaml

Input

Name	Type & Properties	Description
--strandedness	string	Forward or reverse strand?
--bam	file
--annotation_gtf	file
--extra_stringtie_args	string	Extra arguments for running StringTie
--stringtie_ignore_gtf	boolean	Perform reference-guided de novo assembly of transcripts using StringTie, i.e. don't restrict to those in GTF file.

Name

Type & Properties

--strandedness

string

--bam

file

--annotation_gtf

file

--extra_stringtie_args

string

--stringtie_ignore_gtf

boolean

Output

Name	Type & Properties	Description
--transcript_gtf	file output
--coverage_gtf	file output
--abundance	file output
--ballgown	file output	for running ballgown

Name

Type & Properties

--transcript_gtf

file

output

--coverage_gtf

file

output

--abundance

file

output

--ballgown

file

output