rsem/rsem_calculate_expression

Description

Calculate expression with RSEM.

Type

bash_script

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
id: "run"  
counts_gene: "$id.$key.counts_gene.results"  
counts_transcripts: "$id.$key.counts_transcripts.results"  
stat: "$id.$key.stat.stat"  
logs: "$id.$key.logs.log"  
bam_star: "$id.$key.bam_star.bam"  
bam_genome: "$id.$key.bam_genome.bam"  
bam_transcript: "$id.$key.bam_transcript.bam"  
publish_dir: "output/"  
EOM

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

Input

Name	Type & Properties	Description
--id	string	Sample ID.
--strandedness	string	Sample strand-specificity. Must be one of unstranded, forward, reverse
--paired	boolean	Paired-end reads or not?
--input	file multiple	Input reads for quantification.
--index	file	RSEM index.
--extra_args	string	Extra rsem-calculate-expression arguments in addition to the defaults.

Name

Type & Properties

--id

string

--strandedness

string

--paired

boolean

--input

file

multiple

--index

file

--extra_args

string

Output

Name	Type & Properties	Description
--counts_gene	file output	Expression counts on gene level
--counts_transcripts	file output	Expression counts on transcript level
--stat	file output	RSEM statistics
--logs	file output	RSEM logs
--bam_star	file output	BAM file generated by STAR (optional)
--bam_genome	file output	Genome BAM file (optional)
--bam_transcript	file output	Transcript BAM file (optional)

Name

Type & Properties

--counts_gene

file

output

--counts_transcripts

file

output

--stat

file

output

--logs

file

output

--bam_star

file

output

--bam_genome

file

output

--bam_transcript

file

output