eset/create_pdata

Description

Create a pdata file by combining the mapping statistics

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/eset/create_pdata/main.nf \  
  -params-file params.yaml

Arguments

Name	Type & Properties	Description
--star_stats_file	file required	Tab-delimited text file containing statistics (per column) that were generated from the STAR log files (Log.final.out, Summary.csv, ReadsPerGene.out.tab). Each entry (row) in the file describes the values for one well (barcode).
--nrReadsNrGenesPerChromPool	file required	Pivot table in tsv format of the combined nrReadsNrGenesPerChrom files from STAR. Describes per chromosome (as columns) the number of reads, as well as the total number of reads per cell barcode and the percentage of nuclear, ERCC and mitochondrial reads.
--output	file output

Name

Type & Properties

--star_stats_file

file

required

--nrReadsNrGenesPerChromPool

file

required

--output

file

output