stats/combine_star_logs

Description

No description provided.

Type

python_script

License

MIT

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

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

nextflow run https://packages.viash-hub.com/vsh/htrnaseq.git \  
  -revision v0.15.0-rc.2 \  
  -main-script target/nextflow/stats/combine_star_logs/main.nf \  
  -params-file params.yaml

Arguments

Name	Type & Properties	Description
--barcodes	string required multiple	Barcodes responding to the respective log files.
--star_logs	file required multiple	Paths to the STAR log files (most frequently called Log.final.out)
--gene_summary_logs	file required multiple	Paths to the Summary.csv files from the STAR Solo output. Can be found in the 'Solo.out/Gene' folder relative to the root of the STAR output directory.
--reads_per_gene_logs	file required multiple	Paths to the 'ReadsPerGene.out.tab' files as output by STAR.
--features_stats	file required multiple	Paths to the 'Features.stats' files from STAR Solo. Can be found in the 'Solo.out/Gene' folder relative to the root of the STAR output directory.
--output	file output	Tab-delimited file describing for each barcode (as the rows), the metrics (as columns) gathered from the different input files.

Name

Type & Properties

--barcodes

string

required

multiple

--star_logs

file

required

multiple

--gene_summary_logs

file

required

multiple

--reads_per_gene_logs

file

required

multiple

--features_stats

file

required

multiple

--output

file

output