stats/generate_pool_statistics

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'  
nrReadsNrGenesPerChrom: [ "processedBamFile_well1.tsv", "processedBamfile_well2.tsv" ]  
nrReadsNrGenesPerChromPool: "$id.$key.nrReadsNrGenesPerChromPool.txt"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/htrnaseq.git \  
  -revision v0.14.7 \  
  -main-script target/nextflow/stats/generate_pool_statistics/main.nf \  
  -params-file params.yaml

Arguments

Name	Type & Properties	Description
--nrReadsNrGenesPerChrom	file multiple	Path to an output file that contains a .tsv formatted table describing per chromosome the number of reads that were mapped to that chromosome (NumberOfReads column) and the number of genes on that chromosome that had at least one read mapped to it (NumberOfGenes).
--nrReadsNrGenesPerChromPool	file output	Pivot table in tsv format of the combined input nrReadsNrGenesPerChrom files. 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.

Name

Type & Properties

--nrReadsNrGenesPerChrom

file

multiple

--nrReadsNrGenesPerChromPool

file

output