Skip to content

qbic-projects/QSARK

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

51 Commits
 
 
 
 
 
 
 
 
 
 

Repository files navigation

Overview

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.

Data

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.md

Disclaimer: The CNV calls for each patient are not uploaded here. The original PCAWG results can be obtained from https://dcc.icgc.org/ .

Code

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

About

Data analysis for sarek paper

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published

Languages