This repository contains the run scripts, relevant result files, and plotting scripts for the benchmarking of nf-ore/sarek 3.x.
There are two folders: data and code.
The data folder contains subfolders for each experiment type, scripts to run the experiment, additional configuration files, and input files needed to plot the data:
├── bam_vs_cram
│ ├── bam
│ └── cram
├── functional
│ ├── germline
│ └── somatic
├── intervals
│ ├── fastp0_intervals20
│ ├── fastp12
│ ├── fastp12_intervals10
│ ├── fastp16_intervals0
│ ├── fastp4_intervals78
│ ├── fastp8_intervals40
│ └── intervals10
├── pcawg_cnvs
│ ├── DO44888
│ ├── DO44889
│ ├── DO44890
│ ├── DO44919
│ └── DO44930
└── readme.mdDisclaimer: The CNV calls for each patient are not uploaded here. The original PCAWG results can be obtained from https://dcc.icgc.org/ .
The code folder contains Rmarkdown scripts, auxiliary files, a yaml file to create the conda environment to run the scripts, and a results folder, which contains the actual output plots. The functions.R file contains various functions used in the scripts.:
├── QBiCLogo.png
├── Rmarkdown_BAM_vs_CRAM.Rmd
├── Rmarkdown_BAM_vs_CRAM.html
├── Rmarkdown_cnvvalidation.Rmd
├── Rmarkdown_cnvvalidation.html
├── Rmarkdown_dataflow.Rmd
├── Rmarkdown_dataflow.html
├── Rmarkdown_functional_benchmark.Rmd
├── Rmarkdown_functional_benchmark.html
├── environment.yml
├── functions.R
├── qbic-style.css
└── results
├── bam_vs_cram
├── cnvs
├── dataflow
├── functional
└── images